Starting phenix.real_space_refine on Wed Mar 5 16:54:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xo9_38523/03_2025/8xo9_38523.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xo9_38523/03_2025/8xo9_38523.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xo9_38523/03_2025/8xo9_38523.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xo9_38523/03_2025/8xo9_38523.map" model { file = "/net/cci-nas-00/data/ceres_data/8xo9_38523/03_2025/8xo9_38523.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xo9_38523/03_2025/8xo9_38523.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.057 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 27 5.16 5 C 1937 2.51 5 N 454 2.21 5 O 490 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 2908 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 2896 Classifications: {'peptide': 392} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 23, 'TRANS': 368} Chain breaks: 1 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 33 Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'E5E': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.79, per 1000 atoms: 0.96 Number of scatterers: 2908 At special positions: 0 Unit cell: (54.4, 71.4, 75.65, 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 27 16.00 O 490 8.00 N 454 7.00 C 1937 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.76 Conformation dependent library (CDL) restraints added in 359.4 milliseconds 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 708 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 0 sheets defined 91.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 19 through 54 removed outlier: 4.147A pdb=" N VAL A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N VAL A 41 " --> pdb=" O LEU A 37 " (cutoff:3.500A) Proline residue: A 42 - end of helix Proline residue: A 45 - end of helix Processing helix chain 'A' and resid 124 through 157 removed outlier: 3.881A pdb=" N LEU A 133 " --> pdb=" O VAL A 129 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N LYS A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ALA A 139 " --> pdb=" O PHE A 135 " (cutoff:3.500A) Proline residue: A 147 - end of helix removed outlier: 3.894A pdb=" N GLY A 150 " --> pdb=" O ASN A 146 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU A 151 " --> pdb=" O PRO A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 178 removed outlier: 3.640A pdb=" N PHE A 166 " --> pdb=" O ILE A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 211 removed outlier: 3.657A pdb=" N LEU A 185 " --> pdb=" O SER A 181 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N MET A 204 " --> pdb=" O SER A 200 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR A 211 " --> pdb=" O LEU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 246 removed outlier: 3.737A pdb=" N ASN A 219 " --> pdb=" O GLU A 215 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY A 222 " --> pdb=" O GLY A 218 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU A 228 " --> pdb=" O ALA A 224 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL A 234 " --> pdb=" O MET A 230 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY A 235 " --> pdb=" O GLY A 231 " (cutoff:3.500A) Proline residue: A 236 - end of helix Processing helix chain 'A' and resid 249 through 269 Processing helix chain 'A' and resid 284 through 290 Processing helix chain 'A' and resid 291 through 312 removed outlier: 4.157A pdb=" N ILE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 323 Processing helix chain 'A' and resid 328 through 333 removed outlier: 4.149A pdb=" N VAL A 332 " --> pdb=" O TRP A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 356 removed outlier: 4.052A pdb=" N ILE A 350 " --> pdb=" O ASN A 346 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N HIS A 353 " --> pdb=" O GLY A 349 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N LYS A 354 " --> pdb=" O ILE A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 375 Processing helix chain 'A' and resid 376 through 378 No H-bonds generated for 'chain 'A' and resid 376 through 378' Processing helix chain 'A' and resid 380 through 383 Processing helix chain 'A' and resid 384 through 414 removed outlier: 3.604A pdb=" N ASN A 388 " --> pdb=" O LEU A 384 " (cutoff:3.500A) Proline residue: A 404 - end of helix Processing helix chain 'A' and resid 417 through 447 removed outlier: 4.342A pdb=" N VAL A 421 " --> pdb=" O VAL A 417 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N TYR A 422 " --> pdb=" O TYR A 418 " (cutoff:3.500A) Proline residue: A 437 - end of helix Processing helix chain 'A' and resid 448 through 464 removed outlier: 3.610A pdb=" N LEU A 452 " --> pdb=" O GLY A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 470 removed outlier: 3.734A pdb=" N PHE A 469 " --> pdb=" O LEU A 466 " (cutoff:3.500A) 244 hydrogen bonds defined for protein. 723 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: 0.75 Time building geometry restraints manager: 0.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 870 1.34 - 1.46: 645 1.46 - 1.58: 1416 1.58 - 1.69: 0 1.69 - 1.81: 46 Bond restraints: 2977 Sorted by residual: bond pdb=" CAJ E5E A 601 " pdb=" OAC E5E A 601 " ideal model delta sigma weight residual 1.350 1.401 -0.051 2.00e-02 2.50e+03 6.57e+00 bond pdb=" N MET A 175 " pdb=" CA MET A 175 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.19e-02 7.06e+03 6.19e+00 bond pdb=" N MET A 431 " pdb=" CA MET A 431 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.83e+00 bond pdb=" N PHE A 176 " pdb=" CA PHE A 176 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.76e+00 bond pdb=" CAI E5E A 601 " pdb=" OAB E5E A 601 " ideal model delta sigma weight residual 1.354 1.401 -0.047 2.00e-02 2.50e+03 5.45e+00 ... (remaining 2972 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 3952 1.93 - 3.86: 73 3.86 - 5.80: 21 5.80 - 7.73: 5 7.73 - 9.66: 2 Bond angle restraints: 4053 Sorted by residual: angle pdb=" C ALA A 177 " pdb=" N PHE A 178 " pdb=" CA PHE A 178 " ideal model delta sigma weight residual 122.86 116.34 6.52 1.53e+00 4.27e-01 1.81e+01 angle pdb=" CA MET A 175 " pdb=" C MET A 175 " pdb=" O MET A 175 " ideal model delta sigma weight residual 120.82 117.57 3.25 1.05e+00 9.07e-01 9.60e+00 angle pdb=" C ASP A 123 " pdb=" N LEU A 124 " pdb=" CA LEU A 124 " ideal model delta sigma weight residual 121.54 127.10 -5.56 1.91e+00 2.74e-01 8.47e+00 angle pdb=" CA ILE A 447 " pdb=" C ILE A 447 " pdb=" N GLY A 448 " ideal model delta sigma weight residual 116.60 120.72 -4.12 1.45e+00 4.76e-01 8.09e+00 angle pdb=" CA PHE A 176 " pdb=" CB PHE A 176 " pdb=" CG PHE A 176 " ideal model delta sigma weight residual 113.80 116.62 -2.82 1.00e+00 1.00e+00 7.97e+00 ... (remaining 4048 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 1539 17.52 - 35.04: 165 35.04 - 52.57: 37 52.57 - 70.09: 2 70.09 - 87.61: 1 Dihedral angle restraints: 1744 sinusoidal: 634 harmonic: 1110 Sorted by residual: dihedral pdb=" CA LEU A 270 " pdb=" C LEU A 270 " pdb=" N GLN A 271 " pdb=" CA GLN A 271 " ideal model delta harmonic sigma weight residual 180.00 160.96 19.04 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CB GLU A 127 " pdb=" CG GLU A 127 " pdb=" CD GLU A 127 " pdb=" OE1 GLU A 127 " ideal model delta sinusoidal sigma weight residual 0.00 -87.61 87.61 1 3.00e+01 1.11e-03 1.02e+01 dihedral pdb=" CA PRO A 42 " pdb=" C PRO A 42 " pdb=" N ILE A 43 " pdb=" CA ILE A 43 " ideal model delta harmonic sigma weight residual -180.00 -164.09 -15.91 0 5.00e+00 4.00e-02 1.01e+01 ... (remaining 1741 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 360 0.044 - 0.088: 104 0.088 - 0.132: 22 0.132 - 0.177: 1 0.177 - 0.221: 2 Chirality restraints: 489 Sorted by residual: chirality pdb=" CA PHE A 176 " pdb=" N PHE A 176 " pdb=" C PHE A 176 " pdb=" CB PHE A 176 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CAL E5E A 601 " pdb=" CAH E5E A 601 " pdb=" CAK E5E A 601 " pdb=" OAD E5E A 601 " both_signs ideal model delta sigma weight residual False -2.31 -2.51 0.20 2.00e-01 2.50e+01 9.88e-01 chirality pdb=" CA PHE A 348 " pdb=" N PHE A 348 " pdb=" C PHE A 348 " pdb=" CB PHE A 348 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.38e-01 ... (remaining 486 not shown) Planarity restraints: 496 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 124 " 0.015 2.00e-02 2.50e+03 3.03e-02 9.17e+00 pdb=" C LEU A 124 " -0.052 2.00e-02 2.50e+03 pdb=" O LEU A 124 " 0.020 2.00e-02 2.50e+03 pdb=" N LEU A 125 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 235 " 0.042 5.00e-02 4.00e+02 6.25e-02 6.26e+00 pdb=" N PRO A 236 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO A 236 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 236 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 473 " 0.034 5.00e-02 4.00e+02 5.15e-02 4.24e+00 pdb=" N PRO A 474 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 474 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 474 " 0.031 5.00e-02 4.00e+02 ... (remaining 493 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 747 2.81 - 3.33: 2964 3.33 - 3.85: 4782 3.85 - 4.38: 4949 4.38 - 4.90: 9157 Nonbonded interactions: 22599 Sorted by model distance: nonbonded pdb=" OG SER A 325 " pdb=" OE1 GLN A 329 " model vdw 2.284 3.040 nonbonded pdb=" OD2 ASP A 33 " pdb=" OG SER A 196 " model vdw 2.519 3.040 nonbonded pdb=" OG SER A 181 " pdb=" N TYR A 182 " model vdw 2.545 3.120 nonbonded pdb=" O ALA A 333 " pdb=" ND2 ASN A 388 " model vdw 2.568 3.120 nonbonded pdb=" O PRO A 473 " pdb=" CA PRO A 474 " model vdw 2.582 2.776 ... (remaining 22594 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: 1.330 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.170 Find NCS groups from input model: 0.030 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 2977 Z= 0.272 Angle : 0.739 9.662 4053 Z= 0.391 Chirality : 0.043 0.221 489 Planarity : 0.006 0.063 496 Dihedral : 14.590 87.612 1036 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.00 % Allowed : 21.12 % Favored : 78.88 % 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: 1.96 (0.44), residues: 388 helix: 1.80 (0.29), residues: 331 sheet: None (None), residues: 0 loop : -1.67 (0.75), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 318 HIS 0.006 0.002 HIS A 53 PHE 0.019 0.002 PHE A 468 TYR 0.013 0.001 TYR A 49 ARG 0.005 0.001 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.275 Fit side-chains REVERT: A 225 LEU cc_start: 0.7535 (mm) cc_final: 0.6771 (tt) REVERT: A 244 GLU cc_start: 0.8694 (tm-30) cc_final: 0.8344 (tm-30) REVERT: A 405 ILE cc_start: 0.8787 (mm) cc_final: 0.8555 (mt) REVERT: A 431 MET cc_start: 0.8307 (mmt) cc_final: 0.8028 (mmt) REVERT: A 459 ILE cc_start: 0.7168 (mt) cc_final: 0.6903 (mm) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.1282 time to fit residues: 7.3289 Evaluate side-chains 44 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 HIS A 192 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.159985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.131079 restraints weight = 3808.286| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.36 r_work: 0.3450 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.0833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2977 Z= 0.256 Angle : 0.684 9.524 4053 Z= 0.335 Chirality : 0.042 0.152 489 Planarity : 0.006 0.054 496 Dihedral : 5.694 36.900 416 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.98 % Allowed : 20.46 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.45), residues: 388 helix: 2.11 (0.30), residues: 324 sheet: None (None), residues: 0 loop : -2.02 (0.70), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 318 HIS 0.004 0.001 HIS A 53 PHE 0.016 0.002 PHE A 348 TYR 0.010 0.001 TYR A 49 ARG 0.002 0.000 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.281 Fit side-chains REVERT: A 405 ILE cc_start: 0.8310 (mm) cc_final: 0.8051 (mt) REVERT: A 431 MET cc_start: 0.7714 (mmt) cc_final: 0.7424 (mmt) REVERT: A 459 ILE cc_start: 0.6317 (OUTLIER) cc_final: 0.6050 (mm) outliers start: 6 outliers final: 3 residues processed: 49 average time/residue: 0.1137 time to fit residues: 7.1865 Evaluate side-chains 47 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 459 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 0.0670 chunk 17 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 32 optimal weight: 0.6980 chunk 14 optimal weight: 6.9990 chunk 30 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.161218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.132460 restraints weight = 3686.430| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 2.32 r_work: 0.3468 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.1166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2977 Z= 0.216 Angle : 0.655 9.555 4053 Z= 0.317 Chirality : 0.041 0.141 489 Planarity : 0.006 0.053 496 Dihedral : 4.962 23.855 416 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.64 % Allowed : 20.13 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.37 (0.45), residues: 388 helix: 2.18 (0.30), residues: 326 sheet: None (None), residues: 0 loop : -1.84 (0.72), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 328 HIS 0.005 0.002 HIS A 53 PHE 0.014 0.002 PHE A 27 TYR 0.009 0.001 TYR A 49 ARG 0.004 0.000 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.313 Fit side-chains REVERT: A 196 SER cc_start: 0.7799 (t) cc_final: 0.7392 (p) REVERT: A 225 LEU cc_start: 0.7073 (mm) cc_final: 0.6150 (tt) REVERT: A 405 ILE cc_start: 0.8348 (mm) cc_final: 0.8080 (mt) REVERT: A 431 MET cc_start: 0.7734 (mmt) cc_final: 0.7444 (mmt) REVERT: A 459 ILE cc_start: 0.6305 (mt) cc_final: 0.6023 (mm) outliers start: 8 outliers final: 4 residues processed: 49 average time/residue: 0.1159 time to fit residues: 7.3523 Evaluate side-chains 45 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 283 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 10 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.157153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.128370 restraints weight = 3825.904| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.28 r_work: 0.3416 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2977 Z= 0.262 Angle : 0.684 9.421 4053 Z= 0.334 Chirality : 0.042 0.146 489 Planarity : 0.006 0.061 496 Dihedral : 4.758 18.694 416 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.30 % Allowed : 19.80 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.45), residues: 388 helix: 2.13 (0.30), residues: 325 sheet: None (None), residues: 0 loop : -1.90 (0.72), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 318 HIS 0.005 0.002 HIS A 53 PHE 0.015 0.002 PHE A 348 TYR 0.009 0.001 TYR A 49 ARG 0.002 0.000 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.325 Fit side-chains REVERT: A 196 SER cc_start: 0.7948 (t) cc_final: 0.7526 (p) REVERT: A 225 LEU cc_start: 0.7335 (mm) cc_final: 0.6339 (tt) REVERT: A 405 ILE cc_start: 0.8546 (mm) cc_final: 0.8278 (mt) REVERT: A 431 MET cc_start: 0.7871 (mmt) cc_final: 0.7582 (mmt) outliers start: 10 outliers final: 7 residues processed: 53 average time/residue: 0.1135 time to fit residues: 7.8090 Evaluate side-chains 50 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 459 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 14 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 19 optimal weight: 0.1980 chunk 11 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.158479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.129981 restraints weight = 3753.010| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 2.25 r_work: 0.3432 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2977 Z= 0.234 Angle : 0.661 9.481 4053 Z= 0.320 Chirality : 0.041 0.140 489 Planarity : 0.006 0.060 496 Dihedral : 4.630 19.033 416 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 4.29 % Allowed : 20.79 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.38 (0.44), residues: 388 helix: 2.21 (0.30), residues: 325 sheet: None (None), residues: 0 loop : -1.93 (0.71), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 318 HIS 0.004 0.001 HIS A 53 PHE 0.014 0.002 PHE A 27 TYR 0.009 0.001 TYR A 49 ARG 0.002 0.000 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 44 time to evaluate : 0.303 Fit side-chains REVERT: A 196 SER cc_start: 0.7888 (t) cc_final: 0.7491 (p) REVERT: A 225 LEU cc_start: 0.7259 (mm) cc_final: 0.6289 (tt) REVERT: A 405 ILE cc_start: 0.8526 (mm) cc_final: 0.8256 (mt) REVERT: A 431 MET cc_start: 0.7858 (mmt) cc_final: 0.7589 (mmt) REVERT: A 459 ILE cc_start: 0.6628 (OUTLIER) cc_final: 0.6341 (mm) outliers start: 13 outliers final: 6 residues processed: 54 average time/residue: 0.1051 time to fit residues: 7.5215 Evaluate side-chains 51 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 459 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 0.3980 chunk 35 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 10 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 16 optimal weight: 0.4980 chunk 9 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 53 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.159332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.130756 restraints weight = 3837.358| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 2.27 r_work: 0.3444 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2977 Z= 0.212 Angle : 0.659 9.508 4053 Z= 0.319 Chirality : 0.041 0.136 489 Planarity : 0.006 0.059 496 Dihedral : 4.510 18.420 416 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.96 % Allowed : 20.79 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.44), residues: 388 helix: 2.28 (0.30), residues: 325 sheet: None (None), residues: 0 loop : -2.04 (0.68), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 328 HIS 0.003 0.001 HIS A 53 PHE 0.015 0.001 PHE A 27 TYR 0.011 0.001 TYR A 49 ARG 0.001 0.000 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 43 time to evaluate : 0.278 Fit side-chains REVERT: A 196 SER cc_start: 0.7886 (t) cc_final: 0.7489 (p) REVERT: A 225 LEU cc_start: 0.7101 (mm) cc_final: 0.6144 (tt) REVERT: A 397 MET cc_start: 0.7181 (OUTLIER) cc_final: 0.6955 (mtm) REVERT: A 405 ILE cc_start: 0.8532 (mm) cc_final: 0.8254 (mt) REVERT: A 459 ILE cc_start: 0.6577 (OUTLIER) cc_final: 0.6272 (mm) outliers start: 12 outliers final: 5 residues processed: 51 average time/residue: 0.1142 time to fit residues: 7.6071 Evaluate side-chains 51 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 397 MET Chi-restraints excluded: chain A residue 459 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 9 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 2 optimal weight: 0.0980 chunk 0 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 36 optimal weight: 0.5980 chunk 38 optimal weight: 0.0000 chunk 15 optimal weight: 0.6980 overall best weight: 0.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.161730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.133118 restraints weight = 3767.864| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 2.26 r_work: 0.3467 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2977 Z= 0.186 Angle : 0.651 9.534 4053 Z= 0.312 Chirality : 0.040 0.131 489 Planarity : 0.006 0.055 496 Dihedral : 4.407 18.795 416 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 4.62 % Allowed : 20.79 % Favored : 74.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.58 (0.44), residues: 388 helix: 2.38 (0.30), residues: 325 sheet: None (None), residues: 0 loop : -2.09 (0.68), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 328 HIS 0.003 0.001 HIS A 353 PHE 0.014 0.001 PHE A 27 TYR 0.011 0.001 TYR A 49 ARG 0.001 0.000 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 48 time to evaluate : 0.285 Fit side-chains REVERT: A 196 SER cc_start: 0.7919 (t) cc_final: 0.7521 (p) REVERT: A 225 LEU cc_start: 0.7060 (mm) cc_final: 0.6121 (tt) REVERT: A 397 MET cc_start: 0.7158 (OUTLIER) cc_final: 0.6958 (mtm) REVERT: A 405 ILE cc_start: 0.8531 (mm) cc_final: 0.8249 (mt) REVERT: A 459 ILE cc_start: 0.6617 (OUTLIER) cc_final: 0.6319 (mm) outliers start: 14 outliers final: 7 residues processed: 58 average time/residue: 0.1171 time to fit residues: 8.6640 Evaluate side-chains 54 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 176 PHE Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 397 MET Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 459 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 31 optimal weight: 1.9990 chunk 21 optimal weight: 0.0970 chunk 38 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 4 optimal weight: 0.0970 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.160692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.132392 restraints weight = 3724.221| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 2.26 r_work: 0.3461 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2977 Z= 0.199 Angle : 0.670 10.175 4053 Z= 0.320 Chirality : 0.041 0.130 489 Planarity : 0.006 0.055 496 Dihedral : 4.244 18.278 416 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.96 % Allowed : 22.77 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.65 (0.45), residues: 388 helix: 2.40 (0.30), residues: 326 sheet: None (None), residues: 0 loop : -2.00 (0.71), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 328 HIS 0.001 0.001 HIS A 53 PHE 0.014 0.001 PHE A 27 TYR 0.011 0.001 TYR A 49 ARG 0.001 0.000 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.306 Fit side-chains REVERT: A 196 SER cc_start: 0.7977 (t) cc_final: 0.7530 (p) REVERT: A 225 LEU cc_start: 0.7063 (mm) cc_final: 0.6095 (tt) REVERT: A 397 MET cc_start: 0.7177 (OUTLIER) cc_final: 0.6953 (mtm) REVERT: A 459 ILE cc_start: 0.6620 (OUTLIER) cc_final: 0.6313 (mm) outliers start: 12 outliers final: 7 residues processed: 58 average time/residue: 0.1189 time to fit residues: 8.7813 Evaluate side-chains 55 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 397 MET Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 459 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 11 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 0.0970 chunk 18 optimal weight: 0.7980 chunk 35 optimal weight: 0.3980 chunk 20 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.161208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.132581 restraints weight = 3759.905| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 2.30 r_work: 0.3453 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2977 Z= 0.208 Angle : 0.679 10.641 4053 Z= 0.324 Chirality : 0.041 0.131 489 Planarity : 0.006 0.056 496 Dihedral : 4.277 18.674 416 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.96 % Allowed : 22.44 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.65 (0.45), residues: 388 helix: 2.38 (0.30), residues: 327 sheet: None (None), residues: 0 loop : -1.94 (0.72), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 328 HIS 0.002 0.001 HIS A 53 PHE 0.015 0.001 PHE A 27 TYR 0.011 0.001 TYR A 49 ARG 0.001 0.000 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 49 time to evaluate : 0.276 Fit side-chains revert: symmetry clash REVERT: A 196 SER cc_start: 0.7983 (t) cc_final: 0.7535 (p) REVERT: A 225 LEU cc_start: 0.6921 (mm) cc_final: 0.5992 (tt) REVERT: A 459 ILE cc_start: 0.6577 (OUTLIER) cc_final: 0.6268 (mm) outliers start: 12 outliers final: 7 residues processed: 58 average time/residue: 0.1180 time to fit residues: 8.6579 Evaluate side-chains 55 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 459 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 38 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.158346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.128995 restraints weight = 3649.274| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.47 r_work: 0.3447 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2977 Z= 0.260 Angle : 0.704 10.588 4053 Z= 0.340 Chirality : 0.042 0.137 489 Planarity : 0.006 0.063 496 Dihedral : 4.397 18.406 416 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.97 % Allowed : 23.43 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.42 (0.44), residues: 388 helix: 2.26 (0.30), residues: 325 sheet: None (None), residues: 0 loop : -2.09 (0.68), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 318 HIS 0.001 0.001 HIS A 53 PHE 0.015 0.002 PHE A 348 TYR 0.010 0.001 TYR A 49 ARG 0.002 0.000 ARG A 155 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.293 Fit side-chains REVERT: A 196 SER cc_start: 0.8060 (t) cc_final: 0.7620 (p) REVERT: A 225 LEU cc_start: 0.6985 (mm) cc_final: 0.6051 (tt) outliers start: 9 outliers final: 8 residues processed: 58 average time/residue: 0.1302 time to fit residues: 9.5377 Evaluate side-chains 55 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 459 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 13 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 37 optimal weight: 0.2980 chunk 8 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 29 optimal weight: 0.0070 chunk 21 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 20 optimal weight: 0.2980 overall best weight: 0.3598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.164245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.135066 restraints weight = 3622.427| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 2.44 r_work: 0.3517 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2977 Z= 0.186 Angle : 0.689 10.512 4053 Z= 0.325 Chirality : 0.040 0.133 489 Planarity : 0.006 0.054 496 Dihedral : 4.355 18.971 416 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.31 % Allowed : 24.42 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.67 (0.44), residues: 388 helix: 2.35 (0.30), residues: 328 sheet: None (None), residues: 0 loop : -1.70 (0.73), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 328 HIS 0.001 0.001 HIS A 414 PHE 0.014 0.001 PHE A 27 TYR 0.008 0.001 TYR A 49 ARG 0.001 0.000 ARG A 357 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1578.48 seconds wall clock time: 27 minutes 54.85 seconds (1674.85 seconds total)