Starting phenix.real_space_refine on Wed Sep 17 03:17:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xsm_38622/09_2025/8xsm_38622.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xsm_38622/09_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_38622/09_2025/8xsm_38622.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xsm_38622/09_2025/8xsm_38622.map" model { file = "/net/cci-nas-00/data/ceres_data/8xsm_38622/09_2025/8xsm_38622.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xsm_38622/09_2025/8xsm_38622.cif" } resolution = 3.01 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 0.75, per 1000 atoms: 0.27 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: 0.28 Conformation dependent library (CDL) restraints added in 119.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.09 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: 0.28 Time building geometry restraints manager: 0.27 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: 2.010 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: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.100 Find NCS groups from input model: 0.010 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:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.190 ------------------------------------------------------------------------------- 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= 0.447 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.004 0.000 ARG A 402 TYR 0.005 0.001 TYR A 430 PHE 0.011 0.001 PHE A 191 TRP 0.005 0.001 TRP A 379 HIS 0.008 0.001 HIS A 398 Details of bonding type rmsd covalent geometry : bond 0.00829 ( 2861) covalent geometry : angle 0.92608 ( 3928) hydrogen bonds : bond 0.15050 ( 206) hydrogen bonds : angle 5.52408 ( 612) *********************** 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 : 0.092 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: 0.0840 time to fit residues: 3.5991 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 : 0.059 ------------------------------------------------------------------------------- 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 24 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.4980 chunk 22 optimal weight: 2.9990 chunk 13 optimal weight: 0.0870 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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 = 0.3673 r_free = 0.3673 target = 0.145513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.118089 restraints weight = 3073.356| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.86 r_work: 0.3237 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.0986 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= 0.141 Angle : 0.603 6.106 3928 Z= 0.291 Chirality : 0.038 0.121 482 Planarity : 0.006 0.041 476 Dihedral : 9.132 56.031 428 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.40 % Allowed : 13.99 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.49 (0.42), residues: 369 helix: 0.96 (0.31), residues: 273 sheet: None (None), residues: 0 loop : -1.38 (0.59), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 8 TYR 0.006 0.001 TYR A 430 PHE 0.009 0.001 PHE A 191 TRP 0.004 0.001 TRP A 68 HIS 0.005 0.001 HIS A 13 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 2861) covalent geometry : angle 0.60337 ( 3928) hydrogen bonds : bond 0.05487 ( 206) hydrogen bonds : angle 4.16185 ( 612) *********************** 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 30 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 26 time to evaluate : 0.097 Fit side-chains REVERT: A 70 ARG cc_start: 0.6832 (mpt180) cc_final: 0.6391 (mmt180) outliers start: 4 outliers final: 3 residues processed: 30 average time/residue: 0.0569 time to fit residues: 2.1944 Evaluate side-chains 27 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 24 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL 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 9 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3774 r_free = 0.3774 target = 0.150600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.124314 restraints weight = 3037.255| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.70 r_work: 0.3354 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.1074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 2861 Z= 0.157 Angle : 0.621 6.061 3928 Z= 0.297 Chirality : 0.039 0.122 482 Planarity : 0.005 0.038 476 Dihedral : 8.623 54.561 424 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.70 % Allowed : 14.69 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.43), residues: 369 helix: 1.43 (0.31), residues: 273 sheet: None (None), residues: 0 loop : -1.25 (0.59), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 142 TYR 0.005 0.001 TYR A 430 PHE 0.009 0.001 PHE A 191 TRP 0.004 0.001 TRP A 24 HIS 0.005 0.001 HIS A 13 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 2861) covalent geometry : angle 0.62053 ( 3928) hydrogen bonds : bond 0.06127 ( 206) hydrogen bonds : angle 4.12417 ( 612) *********************** 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 28 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 26 time to evaluate : 0.116 Fit side-chains REVERT: A 70 ARG cc_start: 0.7014 (mpt180) cc_final: 0.6539 (mmt180) REVERT: A 272 LEU cc_start: 0.7992 (mm) cc_final: 0.7791 (mm) outliers start: 2 outliers final: 2 residues processed: 28 average time/residue: 0.0474 time to fit residues: 1.8184 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 : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 347 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 25 optimal weight: 1.9990 chunk 33 optimal weight: 0.3980 chunk 3 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 36 optimal weight: 0.4980 chunk 15 optimal weight: 0.7980 chunk 16 optimal weight: 0.3980 chunk 35 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 20 optimal weight: 0.0270 overall best weight: 0.3838 ------------------------------------------------------------------------------- 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 = 0.3663 r_free = 0.3663 target = 0.146162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.118477 restraints weight = 2993.166| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 1.88 r_work: 0.3247 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.1408 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= 0.122 Angle : 0.553 6.089 3928 Z= 0.266 Chirality : 0.036 0.115 482 Planarity : 0.005 0.037 476 Dihedral : 8.003 56.161 424 Min Nonbonded Distance : 2.662 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.75 % Allowed : 13.99 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.81 (0.44), residues: 369 helix: 1.98 (0.31), residues: 272 sheet: None (None), residues: 0 loop : -1.10 (0.60), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 142 TYR 0.004 0.001 TYR A 50 PHE 0.007 0.001 PHE A 348 TRP 0.005 0.001 TRP A 68 HIS 0.004 0.001 HIS A 13 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 2861) covalent geometry : angle 0.55254 ( 3928) hydrogen bonds : bond 0.04573 ( 206) hydrogen bonds : angle 3.90976 ( 612) *********************** 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 28 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 23 time to evaluate : 0.104 Fit side-chains REVERT: A 70 ARG cc_start: 0.6712 (mpt180) cc_final: 0.6235 (mmt180) REVERT: A 345 LEU cc_start: 0.5796 (mt) cc_final: 0.5531 (tp) outliers start: 5 outliers final: 4 residues processed: 28 average time/residue: 0.0630 time to fit residues: 2.2419 Evaluate side-chains 26 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 22 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 20 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 6 optimal weight: 0.2980 chunk 7 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 34 optimal weight: 0.0980 chunk 36 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.3645 r_free = 0.3645 target = 0.144388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.116701 restraints weight = 2980.808| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 1.87 r_work: 0.3246 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.1402 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= 0.133 Angle : 0.563 6.073 3928 Z= 0.271 Chirality : 0.037 0.117 482 Planarity : 0.005 0.037 476 Dihedral : 7.837 56.485 424 Min Nonbonded Distance : 2.658 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.75 % Allowed : 13.64 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.97 (0.44), residues: 369 helix: 2.12 (0.31), residues: 272 sheet: None (None), residues: 0 loop : -1.11 (0.60), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 142 TYR 0.004 0.001 TYR A 430 PHE 0.008 0.001 PHE A 348 TRP 0.005 0.001 TRP A 68 HIS 0.004 0.001 HIS A 13 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 2861) covalent geometry : angle 0.56348 ( 3928) hydrogen bonds : bond 0.05120 ( 206) hydrogen bonds : angle 3.94369 ( 612) *********************** 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 26 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 21 time to evaluate : 0.100 Fit side-chains REVERT: A 70 ARG cc_start: 0.6672 (mpt180) cc_final: 0.6196 (mmt180) REVERT: A 345 LEU cc_start: 0.5704 (mt) cc_final: 0.5467 (tp) REVERT: A 354 MET cc_start: 0.7643 (ttp) cc_final: 0.7314 (tpp) outliers start: 5 outliers final: 4 residues processed: 26 average time/residue: 0.0553 time to fit residues: 1.8753 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 : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 15 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 6 optimal weight: 0.4980 chunk 13 optimal weight: 0.2980 chunk 28 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.3633 r_free = 0.3633 target = 0.143505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.115492 restraints weight = 3022.847| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.89 r_work: 0.3241 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.1496 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= 0.132 Angle : 0.557 6.048 3928 Z= 0.269 Chirality : 0.037 0.117 482 Planarity : 0.005 0.037 476 Dihedral : 7.530 58.152 424 Min Nonbonded Distance : 2.653 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.75 % Allowed : 13.64 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.07 (0.44), residues: 369 helix: 2.20 (0.31), residues: 274 sheet: None (None), residues: 0 loop : -1.19 (0.59), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 142 TYR 0.003 0.001 TYR A 430 PHE 0.007 0.001 PHE A 348 TRP 0.005 0.001 TRP A 68 HIS 0.004 0.001 HIS A 13 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 2861) covalent geometry : angle 0.55726 ( 3928) hydrogen bonds : bond 0.05038 ( 206) hydrogen bonds : angle 3.91718 ( 612) *********************** 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 26 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 21 time to evaluate : 0.095 Fit side-chains REVERT: A 70 ARG cc_start: 0.6613 (mpt180) cc_final: 0.6156 (mmt180) REVERT: A 345 LEU cc_start: 0.5765 (mt) cc_final: 0.5526 (tp) REVERT: A 354 MET cc_start: 0.7659 (ttp) cc_final: 0.7327 (tpp) outliers start: 5 outliers final: 4 residues processed: 26 average time/residue: 0.0570 time to fit residues: 1.9335 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 : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 32 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 6 optimal weight: 0.3980 chunk 17 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 = 0.3643 r_free = 0.3643 target = 0.143896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.116081 restraints weight = 2971.476| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 1.88 r_work: 0.3175 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2861 Z= 0.148 Angle : 0.578 5.607 3928 Z= 0.280 Chirality : 0.038 0.120 482 Planarity : 0.005 0.039 476 Dihedral : 7.634 57.442 424 Min Nonbonded Distance : 2.656 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.98 (0.44), residues: 369 helix: 2.12 (0.31), residues: 274 sheet: None (None), residues: 0 loop : -1.18 (0.59), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 142 TYR 0.004 0.001 TYR A 430 PHE 0.008 0.001 PHE A 19 TRP 0.005 0.001 TRP A 68 HIS 0.004 0.001 HIS A 13 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 2861) covalent geometry : angle 0.57817 ( 3928) hydrogen bonds : bond 0.05716 ( 206) hydrogen bonds : angle 3.99521 ( 612) *********************** 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 26 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 20 time to evaluate : 0.108 Fit side-chains REVERT: A 70 ARG cc_start: 0.6729 (mpt180) cc_final: 0.6289 (mmt180) REVERT: A 345 LEU cc_start: 0.5844 (mt) cc_final: 0.5590 (tp) outliers start: 6 outliers final: 5 residues processed: 26 average time/residue: 0.0588 time to fit residues: 1.9895 Evaluate side-chains 25 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 20 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 30 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 36 optimal weight: 0.0000 chunk 19 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 overall best weight: 0.5584 ------------------------------------------------------------------------------- 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 = 0.3657 r_free = 0.3657 target = 0.145114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.117336 restraints weight = 3041.689| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 1.90 r_work: 0.3213 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.1539 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= 0.136 Angle : 0.559 5.615 3928 Z= 0.271 Chirality : 0.037 0.118 482 Planarity : 0.005 0.039 476 Dihedral : 7.499 58.572 424 Min Nonbonded Distance : 2.654 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.13 (0.44), residues: 369 helix: 2.24 (0.31), residues: 274 sheet: None (None), residues: 0 loop : -1.15 (0.59), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 142 TYR 0.004 0.001 TYR A 430 PHE 0.007 0.001 PHE A 191 TRP 0.005 0.001 TRP A 68 HIS 0.004 0.001 HIS A 13 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 2861) covalent geometry : angle 0.55860 ( 3928) hydrogen bonds : bond 0.05222 ( 206) hydrogen bonds : angle 3.93159 ( 612) *********************** 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 27 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 21 time to evaluate : 0.097 Fit side-chains REVERT: A 70 ARG cc_start: 0.6677 (mpt180) cc_final: 0.6270 (mmt180) REVERT: A 345 LEU cc_start: 0.5794 (mt) cc_final: 0.5554 (tp) outliers start: 6 outliers final: 4 residues processed: 27 average time/residue: 0.0795 time to fit residues: 2.6111 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 : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 27 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 3 optimal weight: 0.0970 chunk 1 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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 = 0.142998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.115158 restraints weight = 3050.273| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 1.89 r_work: 0.3164 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2861 Z= 0.142 Angle : 0.568 5.563 3928 Z= 0.275 Chirality : 0.037 0.118 482 Planarity : 0.005 0.039 476 Dihedral : 7.531 58.888 424 Min Nonbonded Distance : 2.655 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.75 % Allowed : 14.69 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.08 (0.44), residues: 369 helix: 2.21 (0.31), residues: 274 sheet: None (None), residues: 0 loop : -1.17 (0.59), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 142 TYR 0.004 0.001 TYR A 430 PHE 0.007 0.001 PHE A 19 TRP 0.005 0.001 TRP A 68 HIS 0.004 0.001 HIS A 13 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 2861) covalent geometry : angle 0.56808 ( 3928) hydrogen bonds : bond 0.05485 ( 206) hydrogen bonds : angle 3.96009 ( 612) *********************** 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 26 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 21 time to evaluate : 0.095 Fit side-chains REVERT: A 70 ARG cc_start: 0.6672 (mpt180) cc_final: 0.6269 (mmt180) REVERT: A 345 LEU cc_start: 0.5814 (mt) cc_final: 0.5574 (tp) outliers start: 5 outliers final: 5 residues processed: 26 average time/residue: 0.0557 time to fit residues: 1.8910 Evaluate side-chains 26 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 21 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 0 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 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 = 0.3603 r_free = 0.3603 target = 0.140727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.112703 restraints weight = 3086.304| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 1.90 r_work: 0.3149 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.1522 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= 0.150 Angle : 0.581 5.602 3928 Z= 0.282 Chirality : 0.038 0.120 482 Planarity : 0.005 0.039 476 Dihedral : 7.580 59.785 424 Min Nonbonded Distance : 2.656 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.75 % Allowed : 14.69 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.98 (0.44), residues: 369 helix: 2.13 (0.31), residues: 274 sheet: None (None), residues: 0 loop : -1.20 (0.58), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 142 TYR 0.004 0.001 TYR A 430 PHE 0.007 0.001 PHE A 19 TRP 0.005 0.001 TRP A 68 HIS 0.004 0.001 HIS A 13 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 2861) covalent geometry : angle 0.58087 ( 3928) hydrogen bonds : bond 0.05804 ( 206) hydrogen bonds : angle 4.01291 ( 612) ********************** 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: 5 poor density : 22 time to evaluate : 0.093 Fit side-chains REVERT: A 70 ARG cc_start: 0.6770 (mpt180) cc_final: 0.6354 (mmt180) REVERT: A 345 LEU cc_start: 0.5870 (mt) cc_final: 0.5612 (tp) outliers start: 5 outliers final: 5 residues processed: 27 average time/residue: 0.0535 time to fit residues: 1.9000 Evaluate side-chains 26 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 21 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 23 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3606 r_free = 0.3606 target = 0.140683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.112861 restraints weight = 3004.339| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.87 r_work: 0.3116 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 2861 Z= 0.169 Angle : 0.609 5.747 3928 Z= 0.295 Chirality : 0.039 0.123 482 Planarity : 0.005 0.039 476 Dihedral : 7.646 58.471 424 Min Nonbonded Distance : 2.658 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.81 (0.43), residues: 369 helix: 2.00 (0.31), residues: 274 sheet: None (None), residues: 0 loop : -1.23 (0.58), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 142 TYR 0.005 0.001 TYR A 430 PHE 0.010 0.001 PHE A 348 TRP 0.006 0.001 TRP A 24 HIS 0.004 0.001 HIS A 13 Details of bonding type rmsd covalent geometry : bond 0.00408 ( 2861) covalent geometry : angle 0.60937 ( 3928) hydrogen bonds : bond 0.06377 ( 206) hydrogen bonds : angle 4.09276 ( 612) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 981.38 seconds wall clock time: 17 minutes 29.26 seconds (1049.26 seconds total)