Starting phenix.real_space_refine on Wed Mar 5 16:37:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xsm_38622/03_2025/8xsm_38622.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xsm_38622/03_2025/8xsm_38622.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xsm_38622/03_2025/8xsm_38622.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xsm_38622/03_2025/8xsm_38622.map" model { file = "/net/cci-nas-00/data/ceres_data/8xsm_38622/03_2025/8xsm_38622.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xsm_38622/03_2025/8xsm_38622.cif" } resolution = 3.01 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= -0.002 sd= 0.139 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 16 5.16 5 C 1842 2.51 5 N 466 2.21 5 O 464 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 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: 2788 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2734 Classifications: {'peptide': 375} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 25, 'TRANS': 349} Chain breaks: 2 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'RBF': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.06, per 1000 atoms: 1.10 Number of scatterers: 2788 At special positions: 0 Unit cell: (73.1, 62.9, 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 16 16.00 O 464 8.00 N 466 7.00 C 1842 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: 0.87 Conformation dependent library (CDL) restraints added in 335.9 milliseconds 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 680 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 1 sheets defined 81.3% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 8 through 22 Processing helix chain 'A' and resid 24 through 39 removed outlier: 3.904A pdb=" N VAL A 32 " --> pdb=" O ASN A 28 " (cutoff:3.500A) Proline residue: A 35 - end of helix removed outlier: 3.862A pdb=" N LYS A 39 " --> pdb=" O PRO A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 58 removed outlier: 3.521A pdb=" N TYR A 50 " --> pdb=" O SER A 46 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL A 53 " --> pdb=" O SER A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 72 removed outlier: 4.212A pdb=" N LEU A 63 " --> pdb=" O ASN A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 98 removed outlier: 4.511A pdb=" N ILE A 81 " --> pdb=" O GLU A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 133 removed outlier: 4.009A pdb=" N ASN A 129 " --> pdb=" O CYS A 125 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N VAL A 130 " --> pdb=" O CYS A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 139 removed outlier: 3.713A pdb=" N HIS A 138 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU A 139 " --> pdb=" O LEU A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 142 No H-bonds generated for 'chain 'A' and resid 140 through 142' Processing helix chain 'A' and resid 143 through 166 removed outlier: 3.993A pdb=" N ALA A 155 " --> pdb=" O GLN A 151 " (cutoff:3.500A) Proline residue: A 158 - end of helix Processing helix chain 'A' and resid 192 through 218 removed outlier: 3.737A pdb=" N PHE A 196 " --> pdb=" O PRO A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 293 removed outlier: 3.854A pdb=" N LEU A 279 " --> pdb=" O ARG A 275 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU A 280 " --> pdb=" O SER A 276 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU A 282 " --> pdb=" O CYS A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 303 removed outlier: 5.740A pdb=" N SER A 299 " --> pdb=" O PRO A 295 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N PHE A 300 " --> pdb=" O ALA A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 331 removed outlier: 3.803A pdb=" N TYR A 310 " --> pdb=" O GLY A 306 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ASN A 321 " --> pdb=" O GLY A 317 " (cutoff:3.500A) Proline residue: A 322 - end of helix Processing helix chain 'A' and resid 335 through 359 removed outlier: 3.907A pdb=" N CYS A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N MET A 354 " --> pdb=" O GLY A 350 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU A 359 " --> pdb=" O ALA A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 398 removed outlier: 3.862A pdb=" N VAL A 372 " --> pdb=" O THR A 368 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL A 373 " --> pdb=" O SER A 369 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N SER A 378 " --> pdb=" O LEU A 374 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TRP A 379 " --> pdb=" O VAL A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 429 removed outlier: 3.532A pdb=" N ALA A 407 " --> pdb=" O PRO A 403 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY A 409 " --> pdb=" O LEU A 405 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE A 412 " --> pdb=" O ALA A 408 " (cutoff:3.500A) Proline residue: A 425 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 102 through 105 206 hydrogen bonds defined for protein. 612 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: 0.78 Time building geometry restraints manager: 0.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 412 1.30 - 1.43: 753 1.43 - 1.55: 1675 1.55 - 1.68: 0 1.68 - 1.81: 21 Bond restraints: 2861 Sorted by residual: bond pdb=" C4 RBF A 501 " pdb=" C4A RBF A 501 " ideal model delta sigma weight residual 1.481 1.343 0.138 2.00e-02 2.50e+03 4.77e+01 bond pdb=" C4 RBF A 502 " pdb=" C4A RBF A 502 " ideal model delta sigma weight residual 1.481 1.353 0.128 2.00e-02 2.50e+03 4.12e+01 bond pdb=" C10 RBF A 501 " pdb=" C4A RBF A 501 " ideal model delta sigma weight residual 1.440 1.337 0.103 2.00e-02 2.50e+03 2.66e+01 bond pdb=" C ALA A 404 " pdb=" O ALA A 404 " ideal model delta sigma weight residual 1.237 1.184 0.053 1.19e-02 7.06e+03 1.96e+01 bond pdb=" C LEU A 406 " pdb=" O LEU A 406 " ideal model delta sigma weight residual 1.237 1.187 0.050 1.17e-02 7.31e+03 1.80e+01 ... (remaining 2856 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 3801 2.37 - 4.73: 100 4.73 - 7.10: 21 7.10 - 9.47: 5 9.47 - 11.84: 1 Bond angle restraints: 3928 Sorted by residual: angle pdb=" C ARG A 402 " pdb=" N PRO A 403 " pdb=" CA PRO A 403 " ideal model delta sigma weight residual 119.05 126.50 -7.45 1.11e+00 8.12e-01 4.50e+01 angle pdb=" N GLY A 400 " pdb=" CA GLY A 400 " pdb=" C GLY A 400 " ideal model delta sigma weight residual 112.73 120.18 -7.45 1.20e+00 6.94e-01 3.86e+01 angle pdb=" C GLY A 399 " pdb=" N GLY A 400 " pdb=" CA GLY A 400 " ideal model delta sigma weight residual 119.98 126.16 -6.18 1.11e+00 8.12e-01 3.10e+01 angle pdb=" C HIS A 398 " pdb=" N GLY A 399 " pdb=" CA GLY A 399 " ideal model delta sigma weight residual 119.98 125.90 -5.92 1.11e+00 8.12e-01 2.84e+01 angle pdb=" C3' RBF A 501 " pdb=" C4' RBF A 501 " pdb=" O4' RBF A 501 " ideal model delta sigma weight residual 113.84 102.00 11.84 3.00e+00 1.11e-01 1.56e+01 ... (remaining 3923 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.40: 1445 13.40 - 26.80: 141 26.80 - 40.20: 50 40.20 - 53.60: 16 53.60 - 66.99: 6 Dihedral angle restraints: 1658 sinusoidal: 600 harmonic: 1058 Sorted by residual: dihedral pdb=" N LEU A 217 " pdb=" CA LEU A 217 " pdb=" CB LEU A 217 " pdb=" CG LEU A 217 " ideal model delta sinusoidal sigma weight residual -180.00 -126.91 -53.09 3 1.50e+01 4.44e-03 9.17e+00 dihedral pdb=" CA LEU A 359 " pdb=" CB LEU A 359 " pdb=" CG LEU A 359 " pdb=" CD1 LEU A 359 " ideal model delta sinusoidal sigma weight residual 60.00 110.69 -50.69 3 1.50e+01 4.44e-03 8.93e+00 dihedral pdb=" CA SER A 301 " pdb=" C SER A 301 " pdb=" N CYS A 302 " pdb=" CA CYS A 302 " ideal model delta harmonic sigma weight residual -180.00 -165.27 -14.73 0 5.00e+00 4.00e-02 8.67e+00 ... (remaining 1655 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 410 0.061 - 0.122: 63 0.122 - 0.183: 3 0.183 - 0.244: 4 0.244 - 0.305: 2 Chirality restraints: 482 Sorted by residual: chirality pdb=" C4' RBF A 501 " pdb=" C3' RBF A 501 " pdb=" C5' RBF A 501 " pdb=" O4' RBF A 501 " both_signs ideal model delta sigma weight residual False -2.27 -2.58 0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" CA LEU A 405 " pdb=" N LEU A 405 " pdb=" C LEU A 405 " pdb=" CB LEU A 405 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" C4' RBF A 502 " pdb=" C3' RBF A 502 " pdb=" C5' RBF A 502 " pdb=" O4' RBF A 502 " both_signs ideal model delta sigma weight residual False -2.27 -2.52 0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 479 not shown) Planarity restraints: 476 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO A 403 " -0.016 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" C PRO A 403 " 0.057 2.00e-02 2.50e+03 pdb=" O PRO A 403 " -0.021 2.00e-02 2.50e+03 pdb=" N ALA A 404 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 404 " -0.011 2.00e-02 2.50e+03 2.19e-02 4.77e+00 pdb=" C ALA A 404 " 0.038 2.00e-02 2.50e+03 pdb=" O ALA A 404 " -0.014 2.00e-02 2.50e+03 pdb=" N LEU A 405 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 405 " 0.010 2.00e-02 2.50e+03 2.01e-02 4.03e+00 pdb=" C LEU A 405 " -0.035 2.00e-02 2.50e+03 pdb=" O LEU A 405 " 0.013 2.00e-02 2.50e+03 pdb=" N LEU A 406 " 0.012 2.00e-02 2.50e+03 ... (remaining 473 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 68 2.71 - 3.26: 2759 3.26 - 3.80: 4197 3.80 - 4.35: 5369 4.35 - 4.90: 9243 Nonbonded interactions: 21636 Sorted by model distance: nonbonded pdb=" O GLN A 270 " pdb=" OG SER A 276 " model vdw 2.161 3.040 nonbonded pdb=" O3' RBF A 501 " pdb=" O5' RBF A 501 " model vdw 2.186 3.040 nonbonded pdb=" O CYS A 125 " pdb=" OG SER A 128 " model vdw 2.251 3.040 nonbonded pdb=" O2' RBF A 501 " pdb=" O4' RBF A 501 " model vdw 2.381 3.040 nonbonded pdb=" O2' RBF A 502 " pdb=" O4' RBF A 502 " model vdw 2.421 3.040 ... (remaining 21631 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: 2.450 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: 12.330 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:3.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 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 : 0.008 0.138 2861 Z= 0.597 Angle : 0.926 11.836 3928 Z= 0.495 Chirality : 0.050 0.305 482 Planarity : 0.007 0.046 476 Dihedral : 13.813 66.994 978 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.40 % Allowed : 11.54 % Favored : 87.06 % 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: -1.76 (0.38), residues: 369 helix: -0.68 (0.27), residues: 278 sheet: None (None), residues: 0 loop : -2.33 (0.58), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 379 HIS 0.008 0.001 HIS A 398 PHE 0.011 0.001 PHE A 191 TYR 0.005 0.001 TYR A 430 ARG 0.004 0.000 ARG A 402 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.284 Fit side-chains REVERT: A 70 ARG cc_start: 0.6940 (mpt180) cc_final: 0.6585 (mmt180) REVERT: A 169 ARG cc_start: 0.6203 (mtp-110) cc_final: 0.5977 (mtm-85) REVERT: A 402 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.8192 (ttt-90) outliers start: 4 outliers final: 1 residues processed: 37 average time/residue: 0.2095 time to fit residues: 9.1172 Evaluate side-chains 29 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 27 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 402 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 31 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 14 optimal weight: 0.5980 chunk 29 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 ASN A 291 ASN A 298 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.142697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.115399 restraints weight = 3060.661| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.84 r_work: 0.3197 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.0867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2861 Z= 0.242 Angle : 0.651 6.517 3928 Z= 0.312 Chirality : 0.039 0.125 482 Planarity : 0.006 0.042 476 Dihedral : 9.477 59.677 428 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.75 % Allowed : 14.34 % Favored : 83.92 % 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: 0.25 (0.42), residues: 369 helix: 0.77 (0.30), residues: 273 sheet: None (None), residues: 0 loop : -1.44 (0.59), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 379 HIS 0.005 0.001 HIS A 13 PHE 0.010 0.001 PHE A 191 TYR 0.007 0.001 TYR A 430 ARG 0.002 0.000 ARG A 8 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 26 time to evaluate : 0.277 Fit side-chains REVERT: A 70 ARG cc_start: 0.6942 (mpt180) cc_final: 0.6507 (mmt180) outliers start: 5 outliers final: 4 residues processed: 31 average time/residue: 0.1218 time to fit residues: 4.9364 Evaluate side-chains 28 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 24 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 347 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 3 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 16 optimal weight: 0.0000 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.145121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.117749 restraints weight = 2995.668| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 1.83 r_work: 0.3229 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2861 Z= 0.197 Angle : 0.590 6.057 3928 Z= 0.284 Chirality : 0.038 0.119 482 Planarity : 0.005 0.039 476 Dihedral : 8.508 53.339 424 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.75 % Allowed : 14.34 % Favored : 83.92 % 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: 1.17 (0.43), residues: 369 helix: 1.50 (0.31), residues: 272 sheet: None (None), residues: 0 loop : -1.27 (0.59), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 68 HIS 0.005 0.001 HIS A 13 PHE 0.009 0.001 PHE A 348 TYR 0.005 0.001 TYR A 430 ARG 0.002 0.000 ARG A 142 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 24 time to evaluate : 0.269 Fit side-chains REVERT: A 70 ARG cc_start: 0.6824 (mpt180) cc_final: 0.6369 (mmt180) REVERT: A 272 LEU cc_start: 0.7564 (mp) cc_final: 0.7257 (mm) outliers start: 5 outliers final: 2 residues processed: 29 average time/residue: 0.1282 time to fit residues: 4.7082 Evaluate side-chains 26 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 24 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 385 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 3 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 17 optimal weight: 0.4980 chunk 19 optimal weight: 0.3980 chunk 0 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.145017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.117522 restraints weight = 3049.735| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.86 r_work: 0.3227 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2861 Z= 0.196 Angle : 0.583 6.054 3928 Z= 0.281 Chirality : 0.037 0.119 482 Planarity : 0.005 0.038 476 Dihedral : 8.253 54.107 424 Min Nonbonded Distance : 2.664 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.45 % Allowed : 13.64 % Favored : 83.92 % 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: 1.51 (0.43), residues: 369 helix: 1.79 (0.31), residues: 273 sheet: None (None), residues: 0 loop : -1.32 (0.57), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 68 HIS 0.005 0.001 HIS A 13 PHE 0.008 0.001 PHE A 348 TYR 0.004 0.001 TYR A 430 ARG 0.002 0.000 ARG A 142 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 24 time to evaluate : 0.267 Fit side-chains REVERT: A 70 ARG cc_start: 0.6882 (mpt180) cc_final: 0.6416 (mmt180) REVERT: A 272 LEU cc_start: 0.7543 (mp) cc_final: 0.7261 (mm) REVERT: A 345 LEU cc_start: 0.5905 (mt) cc_final: 0.5668 (tp) outliers start: 7 outliers final: 5 residues processed: 31 average time/residue: 0.1112 time to fit residues: 4.5851 Evaluate side-chains 27 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 22 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 347 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 18 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.142311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.114786 restraints weight = 3041.864| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.85 r_work: 0.3227 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2861 Z= 0.213 Angle : 0.593 6.013 3928 Z= 0.286 Chirality : 0.038 0.120 482 Planarity : 0.005 0.038 476 Dihedral : 8.144 54.383 424 Min Nonbonded Distance : 2.658 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.45 % Allowed : 13.64 % Favored : 83.92 % 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: 1.65 (0.43), residues: 369 helix: 1.85 (0.31), residues: 274 sheet: None (None), residues: 0 loop : -1.18 (0.59), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 68 HIS 0.004 0.001 HIS A 13 PHE 0.008 0.001 PHE A 348 TYR 0.005 0.001 TYR A 430 ARG 0.002 0.000 ARG A 142 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 23 time to evaluate : 0.287 Fit side-chains REVERT: A 70 ARG cc_start: 0.6915 (mpt180) cc_final: 0.6471 (mmt180) REVERT: A 272 LEU cc_start: 0.7580 (mp) cc_final: 0.7290 (mm) REVERT: A 345 LEU cc_start: 0.5881 (mt) cc_final: 0.5658 (tp) outliers start: 7 outliers final: 6 residues processed: 30 average time/residue: 0.1220 time to fit residues: 4.9113 Evaluate side-chains 29 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 23 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 385 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 24 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 36 optimal weight: 0.0980 chunk 9 optimal weight: 2.9990 chunk 35 optimal weight: 0.0980 chunk 30 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 13 optimal weight: 0.2980 chunk 4 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.147908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.120530 restraints weight = 3032.015| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.85 r_work: 0.3281 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2861 Z= 0.159 Angle : 0.543 6.040 3928 Z= 0.262 Chirality : 0.036 0.115 482 Planarity : 0.005 0.037 476 Dihedral : 7.620 58.055 424 Min Nonbonded Distance : 2.653 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.10 % Allowed : 14.34 % Favored : 83.57 % 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: 2.19 (0.44), residues: 369 helix: 2.27 (0.31), residues: 272 sheet: None (None), residues: 0 loop : -0.98 (0.61), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 68 HIS 0.004 0.001 HIS A 13 PHE 0.008 0.001 PHE A 348 TYR 0.004 0.001 TYR A 50 ARG 0.001 0.000 ARG A 142 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 21 time to evaluate : 0.243 Fit side-chains REVERT: A 70 ARG cc_start: 0.6775 (mpt180) cc_final: 0.6333 (mmt180) REVERT: A 272 LEU cc_start: 0.7567 (mp) cc_final: 0.7280 (mm) REVERT: A 345 LEU cc_start: 0.5893 (mt) cc_final: 0.5647 (tp) REVERT: A 354 MET cc_start: 0.7714 (ttp) cc_final: 0.7393 (tpp) outliers start: 6 outliers final: 4 residues processed: 27 average time/residue: 0.1219 time to fit residues: 4.3673 Evaluate side-chains 25 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 385 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 21 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 36 optimal weight: 0.2980 chunk 32 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.144513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.116877 restraints weight = 3078.487| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.87 r_work: 0.3234 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2861 Z= 0.200 Angle : 0.572 6.018 3928 Z= 0.277 Chirality : 0.037 0.119 482 Planarity : 0.005 0.038 476 Dihedral : 7.688 57.413 424 Min Nonbonded Distance : 2.656 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.10 % Allowed : 13.99 % Favored : 83.92 % 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: 2.02 (0.44), residues: 369 helix: 2.13 (0.31), residues: 274 sheet: None (None), residues: 0 loop : -1.09 (0.60), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 68 HIS 0.004 0.001 HIS A 13 PHE 0.008 0.001 PHE A 348 TYR 0.004 0.001 TYR A 430 ARG 0.001 0.000 ARG A 142 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 22 time to evaluate : 0.304 Fit side-chains REVERT: A 70 ARG cc_start: 0.6817 (mpt180) cc_final: 0.6386 (mmt180) REVERT: A 272 LEU cc_start: 0.7596 (mp) cc_final: 0.7304 (mm) REVERT: A 345 LEU cc_start: 0.5889 (mt) cc_final: 0.5645 (tp) outliers start: 6 outliers final: 6 residues processed: 28 average time/residue: 0.1268 time to fit residues: 4.7085 Evaluate side-chains 28 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 22 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 385 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 33 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 36 optimal weight: 0.4980 chunk 17 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.144202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.116683 restraints weight = 3027.846| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.86 r_work: 0.3232 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2861 Z= 0.204 Angle : 0.577 6.003 3928 Z= 0.279 Chirality : 0.038 0.119 482 Planarity : 0.005 0.038 476 Dihedral : 7.647 58.373 424 Min Nonbonded Distance : 2.655 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.45 % Allowed : 13.99 % Favored : 83.57 % 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: 2.01 (0.44), residues: 369 helix: 2.13 (0.31), residues: 274 sheet: None (None), residues: 0 loop : -1.11 (0.60), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 68 HIS 0.004 0.001 HIS A 13 PHE 0.008 0.001 PHE A 348 TYR 0.004 0.001 TYR A 430 ARG 0.001 0.000 ARG A 334 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 23 time to evaluate : 0.293 Fit side-chains REVERT: A 70 ARG cc_start: 0.6790 (mpt180) cc_final: 0.6383 (mmt180) REVERT: A 272 LEU cc_start: 0.7607 (mp) cc_final: 0.7309 (mm) REVERT: A 345 LEU cc_start: 0.5917 (mt) cc_final: 0.5665 (tp) outliers start: 7 outliers final: 7 residues processed: 30 average time/residue: 0.1186 time to fit residues: 4.8090 Evaluate side-chains 29 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 22 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 385 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 31 optimal weight: 0.7980 chunk 17 optimal weight: 0.0670 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 6 optimal weight: 0.0010 chunk 15 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.5724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.145371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.117750 restraints weight = 3057.445| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.87 r_work: 0.3246 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2861 Z= 0.188 Angle : 0.562 6.004 3928 Z= 0.273 Chirality : 0.037 0.117 482 Planarity : 0.005 0.038 476 Dihedral : 7.547 59.965 424 Min Nonbonded Distance : 2.654 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.10 % Allowed : 14.34 % Favored : 83.57 % 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: 2.15 (0.44), residues: 369 helix: 2.24 (0.31), residues: 274 sheet: None (None), residues: 0 loop : -1.09 (0.60), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 68 HIS 0.004 0.001 HIS A 13 PHE 0.008 0.001 PHE A 348 TYR 0.004 0.001 TYR A 430 ARG 0.001 0.000 ARG A 142 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 22 time to evaluate : 0.301 Fit side-chains REVERT: A 70 ARG cc_start: 0.6788 (mpt180) cc_final: 0.6387 (mmt180) REVERT: A 272 LEU cc_start: 0.7593 (mp) cc_final: 0.7296 (mm) REVERT: A 345 LEU cc_start: 0.5926 (mt) cc_final: 0.5683 (tp) outliers start: 6 outliers final: 6 residues processed: 28 average time/residue: 0.1424 time to fit residues: 5.3455 Evaluate side-chains 28 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 22 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 385 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 18 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 16 optimal weight: 0.4980 chunk 26 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 6 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 13 optimal weight: 0.2980 chunk 2 optimal weight: 0.9990 chunk 28 optimal weight: 0.0010 overall best weight: 0.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.147134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.119506 restraints weight = 3067.009| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.88 r_work: 0.3268 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2861 Z= 0.168 Angle : 0.544 6.009 3928 Z= 0.264 Chirality : 0.036 0.115 482 Planarity : 0.005 0.038 476 Dihedral : 7.364 59.948 424 Min Nonbonded Distance : 2.654 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.10 % Allowed : 14.69 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.44), residues: 369 helix: 2.40 (0.31), residues: 273 sheet: None (None), residues: 0 loop : -1.11 (0.59), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 68 HIS 0.004 0.001 HIS A 13 PHE 0.008 0.001 PHE A 348 TYR 0.003 0.001 TYR A 50 ARG 0.001 0.000 ARG A 142 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 21 time to evaluate : 0.299 Fit side-chains REVERT: A 70 ARG cc_start: 0.6802 (mpt180) cc_final: 0.6407 (mmt180) REVERT: A 272 LEU cc_start: 0.7600 (mp) cc_final: 0.7313 (mm) REVERT: A 345 LEU cc_start: 0.5898 (mt) cc_final: 0.5670 (tp) REVERT: A 354 MET cc_start: 0.7728 (ttp) cc_final: 0.7394 (tpp) outliers start: 6 outliers final: 6 residues processed: 27 average time/residue: 0.1229 time to fit residues: 4.4050 Evaluate side-chains 27 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 21 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 385 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 35 optimal weight: 0.0470 chunk 17 optimal weight: 0.0970 chunk 25 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 overall best weight: 0.4476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.147202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.119643 restraints weight = 3004.262| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.86 r_work: 0.3279 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2861 Z= 0.172 Angle : 0.540 5.487 3928 Z= 0.262 Chirality : 0.036 0.115 482 Planarity : 0.005 0.039 476 Dihedral : 7.218 58.783 424 Min Nonbonded Distance : 2.653 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.10 % Allowed : 14.34 % Favored : 83.57 % 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: 2.40 (0.44), residues: 369 helix: 2.39 (0.31), residues: 276 sheet: None (None), residues: 0 loop : -0.96 (0.61), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 68 HIS 0.004 0.001 HIS A 13 PHE 0.007 0.001 PHE A 348 TYR 0.003 0.001 TYR A 50 ARG 0.001 0.000 ARG A 142 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1809.25 seconds wall clock time: 31 minutes 42.01 seconds (1902.01 seconds total)