Starting phenix.real_space_refine on Fri Aug 22 14:48:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hff_34719/08_2025/8hff_34719.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hff_34719/08_2025/8hff_34719.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8hff_34719/08_2025/8hff_34719.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hff_34719/08_2025/8hff_34719.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hff_34719/08_2025/8hff_34719.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hff_34719/08_2025/8hff_34719.map" } resolution = 2.86 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= -0.000 sd= 0.127 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 20 5.16 5 C 2953 2.51 5 N 681 2.21 5 O 745 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4399 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4373 Classifications: {'peptide': 547} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 527} Chain breaks: 1 Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Unusual residues: {'LNR': 2} Classifications: {'undetermined': 2, 'water': 2} Link IDs: {None: 3} Time building chain proxies: 1.35, per 1000 atoms: 0.31 Number of scatterers: 4399 At special positions: 0 Unit cell: (70.3625, 69.28, 98.5075, 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 20 16.00 O 745 8.00 N 681 7.00 C 2953 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 176 " - pdb=" SG CYS A 185 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.29 Conformation dependent library (CDL) restraints added in 110.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1006 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 1 sheets defined 82.6% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 60 through 74 Processing helix chain 'A' and resid 75 through 89 removed outlier: 3.649A pdb=" N VAL A 79 " --> pdb=" O ASP A 75 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N PHE A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) Proline residue: A 83 - end of helix Processing helix chain 'A' and resid 94 through 105 Processing helix chain 'A' and resid 105 through 121 Processing helix chain 'A' and resid 125 through 130 removed outlier: 3.691A pdb=" N TRP A 128 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE A 130 " --> pdb=" O VAL A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 133 No H-bonds generated for 'chain 'A' and resid 131 through 133' Processing helix chain 'A' and resid 134 through 166 Processing helix chain 'A' and resid 208 through 217 Processing helix chain 'A' and resid 220 through 224 Processing helix chain 'A' and resid 234 through 253 Processing helix chain 'A' and resid 255 through 261 removed outlier: 3.639A pdb=" N THR A 258 " --> pdb=" O GLY A 255 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LYS A 261 " --> pdb=" O THR A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 283 removed outlier: 3.817A pdb=" N THR A 266 " --> pdb=" O VAL A 262 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR A 268 " --> pdb=" O TRP A 264 " (cutoff:3.500A) Proline residue: A 270 - end of helix removed outlier: 3.906A pdb=" N THR A 283 " --> pdb=" O VAL A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 296 removed outlier: 3.714A pdb=" N GLY A 290 " --> pdb=" O GLY A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 303 Processing helix chain 'A' and resid 305 through 319 Processing helix chain 'A' and resid 324 through 332 removed outlier: 3.968A pdb=" N TYR A 332 " --> pdb=" O ALA A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 373 Processing helix chain 'A' and resid 385 through 396 Proline residue: A 392 - end of helix Processing helix chain 'A' and resid 400 through 435 removed outlier: 3.615A pdb=" N TRP A 404 " --> pdb=" O GLY A 400 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP A 434 " --> pdb=" O GLY A 430 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE A 435 " --> pdb=" O LEU A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 440 Processing helix chain 'A' and resid 441 through 459 Processing helix chain 'A' and resid 464 through 476 removed outlier: 3.796A pdb=" N VAL A 468 " --> pdb=" O GLY A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 497 Processing helix chain 'A' and resid 497 through 510 Processing helix chain 'A' and resid 514 through 523 Processing helix chain 'A' and resid 523 through 539 Processing helix chain 'A' and resid 551 through 567 removed outlier: 3.587A pdb=" N ASN A 555 " --> pdb=" O PRO A 551 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER A 565 " --> pdb=" O ILE A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 580 removed outlier: 3.507A pdb=" N ILE A 571 " --> pdb=" O VAL A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 593 Processing helix chain 'A' and resid 594 through 604 removed outlier: 4.040A pdb=" N HIS A 598 " --> pdb=" O GLU A 595 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N HIS A 599 " --> pdb=" O ASN A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 609 Processing helix chain 'A' and resid 610 through 615 removed outlier: 3.759A pdb=" N TRP A 614 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 544 through 545 302 hydrogen bonds defined for protein. 867 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.72 Time building geometry restraints manager: 0.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 649 1.29 - 1.42: 1370 1.42 - 1.55: 2488 1.55 - 1.68: 0 1.68 - 1.81: 31 Bond restraints: 4538 Sorted by residual: bond pdb=" C GLY A 92 " pdb=" O GLY A 92 " ideal model delta sigma weight residual 1.235 1.161 0.074 1.35e-02 5.49e+03 2.98e+01 bond pdb=" C ASN A 89 " pdb=" O ASN A 89 " ideal model delta sigma weight residual 1.232 1.167 0.065 1.36e-02 5.41e+03 2.31e+01 bond pdb=" C GLY A 92 " pdb=" N ALA A 93 " ideal model delta sigma weight residual 1.332 1.268 0.064 1.40e-02 5.10e+03 2.09e+01 bond pdb=" C GLY A 91 " pdb=" O GLY A 91 " ideal model delta sigma weight residual 1.235 1.186 0.048 1.35e-02 5.49e+03 1.28e+01 bond pdb=" C GLY A 90 " pdb=" O GLY A 90 " ideal model delta sigma weight residual 1.235 1.191 0.043 1.35e-02 5.49e+03 1.03e+01 ... (remaining 4533 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 6006 1.31 - 2.61: 131 2.61 - 3.92: 40 3.92 - 5.22: 12 5.22 - 6.53: 1 Bond angle restraints: 6190 Sorted by residual: angle pdb=" CA ASN A 89 " pdb=" C ASN A 89 " pdb=" O ASN A 89 " ideal model delta sigma weight residual 121.17 117.39 3.78 1.24e+00 6.50e-01 9.29e+00 angle pdb=" N GLY A 90 " pdb=" CA GLY A 90 " pdb=" C GLY A 90 " ideal model delta sigma weight residual 113.18 119.71 -6.53 2.37e+00 1.78e-01 7.59e+00 angle pdb=" C ASN A 89 " pdb=" CA ASN A 89 " pdb=" CB ASN A 89 " ideal model delta sigma weight residual 111.23 115.90 -4.67 1.70e+00 3.46e-01 7.53e+00 angle pdb=" C PHE A 150 " pdb=" N TYR A 151 " pdb=" CA TYR A 151 " ideal model delta sigma weight residual 121.14 116.53 4.61 1.75e+00 3.27e-01 6.93e+00 angle pdb=" CA TYR A 151 " pdb=" CB TYR A 151 " pdb=" CG TYR A 151 " ideal model delta sigma weight residual 113.90 118.52 -4.62 1.80e+00 3.09e-01 6.59e+00 ... (remaining 6185 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 2209 17.79 - 35.58: 251 35.58 - 53.37: 61 53.37 - 71.16: 15 71.16 - 88.95: 1 Dihedral angle restraints: 2537 sinusoidal: 957 harmonic: 1580 Sorted by residual: dihedral pdb=" CA ILE A 103 " pdb=" C ILE A 103 " pdb=" N ILE A 104 " pdb=" CA ILE A 104 " ideal model delta harmonic sigma weight residual -180.00 -158.47 -21.53 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" C TYR A 205 " pdb=" N TYR A 205 " pdb=" CA TYR A 205 " pdb=" CB TYR A 205 " ideal model delta harmonic sigma weight residual -122.60 -131.34 8.74 0 2.50e+00 1.60e-01 1.22e+01 dihedral pdb=" CA ASP A 64 " pdb=" CB ASP A 64 " pdb=" CG ASP A 64 " pdb=" OD1 ASP A 64 " ideal model delta sinusoidal sigma weight residual -30.00 -89.91 59.91 1 2.00e+01 2.50e-03 1.20e+01 ... (remaining 2534 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 633 0.067 - 0.135: 54 0.135 - 0.202: 3 0.202 - 0.270: 0 0.270 - 0.337: 1 Chirality restraints: 691 Sorted by residual: chirality pdb=" CA TYR A 205 " pdb=" N TYR A 205 " pdb=" C TYR A 205 " pdb=" CB TYR A 205 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.84e+00 chirality pdb=" CB VAL A 70 " pdb=" CA VAL A 70 " pdb=" CG1 VAL A 70 " pdb=" CG2 VAL A 70 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.16 2.00e-01 2.50e+01 6.78e-01 chirality pdb=" CAL LNR A 702 " pdb=" CAH LNR A 702 " pdb=" CAK LNR A 702 " pdb=" OAD LNR A 702 " both_signs ideal model delta sigma weight residual False -2.28 -2.43 0.15 2.00e-01 2.50e+01 5.38e-01 ... (remaining 688 not shown) Planarity restraints: 751 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 103 " 0.017 2.00e-02 2.50e+03 3.44e-02 1.19e+01 pdb=" C ILE A 103 " -0.060 2.00e-02 2.50e+03 pdb=" O ILE A 103 " 0.022 2.00e-02 2.50e+03 pdb=" N ILE A 104 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 89 " -0.016 2.00e-02 2.50e+03 3.22e-02 1.03e+01 pdb=" C ASN A 89 " 0.056 2.00e-02 2.50e+03 pdb=" O ASN A 89 " -0.021 2.00e-02 2.50e+03 pdb=" N GLY A 90 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 88 " 0.015 2.00e-02 2.50e+03 2.94e-02 8.62e+00 pdb=" C LYS A 88 " -0.051 2.00e-02 2.50e+03 pdb=" O LYS A 88 " 0.019 2.00e-02 2.50e+03 pdb=" N ASN A 89 " 0.017 2.00e-02 2.50e+03 ... (remaining 748 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 79 2.69 - 3.25: 4446 3.25 - 3.80: 7147 3.80 - 4.35: 9270 4.35 - 4.90: 16096 Nonbonded interactions: 37038 Sorted by model distance: nonbonded pdb=" OD1 ASP A 75 " pdb=" OG SER A 419 " model vdw 2.142 3.040 nonbonded pdb=" O ALA A 328 " pdb=" OG SER A 331 " model vdw 2.265 3.040 nonbonded pdb=" OD1 ASN A 337 " pdb=" N ASN A 338 " model vdw 2.287 3.120 nonbonded pdb=" O THR A 283 " pdb=" OG1 THR A 283 " model vdw 2.327 3.040 nonbonded pdb=" N ASP A 175 " pdb=" OD1 ASP A 175 " model vdw 2.367 3.120 ... (remaining 37033 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: 0.700 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.230 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 4539 Z= 0.217 Angle : 0.544 6.527 6192 Z= 0.292 Chirality : 0.040 0.337 691 Planarity : 0.004 0.039 751 Dihedral : 16.022 88.952 1528 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.08 % Allowed : 19.52 % Favored : 79.39 % 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: 1.96 (0.38), residues: 543 helix: 1.68 (0.28), residues: 376 sheet: None (None), residues: 0 loop : 0.60 (0.53), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 607 TYR 0.018 0.001 TYR A 151 PHE 0.009 0.001 PHE A 362 TRP 0.008 0.001 TRP A 553 HIS 0.001 0.000 HIS A 296 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 4538) covalent geometry : angle 0.54388 ( 6190) SS BOND : bond 0.00176 ( 1) SS BOND : angle 0.56834 ( 2) hydrogen bonds : bond 0.12187 ( 302) hydrogen bonds : angle 5.45337 ( 867) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.196 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 57 average time/residue: 0.3953 time to fit residues: 23.9348 Evaluate side-chains 54 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 498 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 26 optimal weight: 0.0670 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 53 optimal weight: 7.9990 chunk 19 optimal weight: 4.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.150709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.116057 restraints weight = 5212.730| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.00 r_work: 0.3200 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.0944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4539 Z= 0.135 Angle : 0.517 7.385 6192 Z= 0.270 Chirality : 0.040 0.147 691 Planarity : 0.004 0.047 751 Dihedral : 5.968 58.730 607 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.39 % Allowed : 16.27 % Favored : 81.34 % 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: 2.02 (0.38), residues: 543 helix: 1.76 (0.27), residues: 382 sheet: None (None), residues: 0 loop : 0.48 (0.54), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 587 TYR 0.015 0.001 TYR A 151 PHE 0.015 0.001 PHE A 101 TRP 0.010 0.001 TRP A 553 HIS 0.001 0.000 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 4538) covalent geometry : angle 0.51720 ( 6190) SS BOND : bond 0.00326 ( 1) SS BOND : angle 0.94701 ( 2) hydrogen bonds : bond 0.04905 ( 302) hydrogen bonds : angle 4.88018 ( 867) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 51 time to evaluate : 0.174 Fit side-chains revert: symmetry clash REVERT: A 329 PHE cc_start: 0.7797 (m-80) cc_final: 0.7456 (m-10) REVERT: A 459 PHE cc_start: 0.7549 (OUTLIER) cc_final: 0.6411 (t80) REVERT: A 506 GLN cc_start: 0.7900 (OUTLIER) cc_final: 0.7098 (tm-30) outliers start: 11 outliers final: 5 residues processed: 58 average time/residue: 0.3402 time to fit residues: 21.1444 Evaluate side-chains 54 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 TYR Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 506 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 26 optimal weight: 0.0040 chunk 48 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 47 optimal weight: 9.9990 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 436 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.150175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.115519 restraints weight = 5202.401| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.00 r_work: 0.3217 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4539 Z= 0.124 Angle : 0.482 6.636 6192 Z= 0.254 Chirality : 0.039 0.144 691 Planarity : 0.004 0.049 751 Dihedral : 5.141 56.136 602 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.95 % Allowed : 16.05 % Favored : 82.00 % 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 (0.37), residues: 543 helix: 1.78 (0.27), residues: 382 sheet: None (None), residues: 0 loop : 0.55 (0.54), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 587 TYR 0.016 0.001 TYR A 151 PHE 0.011 0.001 PHE A 110 TRP 0.009 0.001 TRP A 553 HIS 0.001 0.000 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 4538) covalent geometry : angle 0.48150 ( 6190) SS BOND : bond 0.00229 ( 1) SS BOND : angle 0.71731 ( 2) hydrogen bonds : bond 0.04660 ( 302) hydrogen bonds : angle 4.74291 ( 867) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.185 Fit side-chains revert: symmetry clash REVERT: A 78 ASN cc_start: 0.8373 (m110) cc_final: 0.8152 (m-40) REVERT: A 329 PHE cc_start: 0.7757 (m-80) cc_final: 0.7421 (m-10) REVERT: A 459 PHE cc_start: 0.7437 (OUTLIER) cc_final: 0.6309 (t80) outliers start: 9 outliers final: 3 residues processed: 58 average time/residue: 0.3310 time to fit residues: 20.5779 Evaluate side-chains 53 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain A residue 459 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 16 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3712 r_free = 0.3712 target = 0.149910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.115574 restraints weight = 5200.232| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.01 r_work: 0.3167 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4539 Z= 0.147 Angle : 0.507 8.004 6192 Z= 0.267 Chirality : 0.040 0.155 691 Planarity : 0.004 0.051 751 Dihedral : 5.128 51.263 602 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.74 % Allowed : 17.79 % Favored : 80.48 % 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: 2.02 (0.37), residues: 543 helix: 1.71 (0.27), residues: 386 sheet: None (None), residues: 0 loop : 0.59 (0.55), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 587 TYR 0.018 0.001 TYR A 84 PHE 0.011 0.001 PHE A 110 TRP 0.008 0.001 TRP A 553 HIS 0.002 0.000 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 4538) covalent geometry : angle 0.50694 ( 6190) SS BOND : bond 0.00244 ( 1) SS BOND : angle 0.74131 ( 2) hydrogen bonds : bond 0.05097 ( 302) hydrogen bonds : angle 4.82666 ( 867) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.162 Fit side-chains revert: symmetry clash REVERT: A 78 ASN cc_start: 0.8394 (m110) cc_final: 0.7923 (m110) REVERT: A 329 PHE cc_start: 0.7816 (m-80) cc_final: 0.7495 (m-10) REVERT: A 459 PHE cc_start: 0.7540 (OUTLIER) cc_final: 0.6414 (t80) REVERT: A 509 MET cc_start: 0.8213 (mtm) cc_final: 0.7857 (mtm) outliers start: 8 outliers final: 4 residues processed: 51 average time/residue: 0.3516 time to fit residues: 19.1697 Evaluate side-chains 47 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain A residue 459 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 43 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 53 optimal weight: 0.0020 chunk 29 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 7 optimal weight: 0.3980 chunk 45 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 ASN A 507 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.147473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.111208 restraints weight = 5297.998| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.13 r_work: 0.3191 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4539 Z= 0.126 Angle : 0.480 6.744 6192 Z= 0.253 Chirality : 0.039 0.145 691 Planarity : 0.004 0.052 751 Dihedral : 4.829 46.248 602 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.39 % Allowed : 17.57 % Favored : 80.04 % 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 (0.37), residues: 543 helix: 1.84 (0.27), residues: 383 sheet: None (None), residues: 0 loop : 0.51 (0.54), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 587 TYR 0.016 0.001 TYR A 84 PHE 0.011 0.001 PHE A 110 TRP 0.009 0.001 TRP A 235 HIS 0.002 0.000 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 4538) covalent geometry : angle 0.48005 ( 6190) SS BOND : bond 0.00230 ( 1) SS BOND : angle 0.66927 ( 2) hydrogen bonds : bond 0.04700 ( 302) hydrogen bonds : angle 4.72089 ( 867) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.163 Fit side-chains revert: symmetry clash REVERT: A 78 ASN cc_start: 0.8326 (m110) cc_final: 0.8021 (m110) REVERT: A 329 PHE cc_start: 0.7746 (m-80) cc_final: 0.7445 (m-10) REVERT: A 459 PHE cc_start: 0.7516 (OUTLIER) cc_final: 0.6413 (t80) outliers start: 11 outliers final: 3 residues processed: 55 average time/residue: 0.3378 time to fit residues: 19.8870 Evaluate side-chains 51 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain A residue 459 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 47 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 24 optimal weight: 0.4980 chunk 9 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 chunk 21 optimal weight: 5.9990 chunk 7 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 507 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.152595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.118542 restraints weight = 5276.713| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.01 r_work: 0.3214 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4539 Z= 0.124 Angle : 0.477 6.970 6192 Z= 0.251 Chirality : 0.039 0.145 691 Planarity : 0.004 0.052 751 Dihedral : 4.408 30.874 600 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.60 % Allowed : 19.09 % Favored : 78.31 % 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: 2.18 (0.37), residues: 543 helix: 1.88 (0.27), residues: 383 sheet: None (None), residues: 0 loop : 0.52 (0.54), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 587 TYR 0.017 0.001 TYR A 151 PHE 0.011 0.001 PHE A 110 TRP 0.009 0.001 TRP A 553 HIS 0.002 0.000 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 4538) covalent geometry : angle 0.47675 ( 6190) SS BOND : bond 0.00227 ( 1) SS BOND : angle 0.67201 ( 2) hydrogen bonds : bond 0.04642 ( 302) hydrogen bonds : angle 4.68098 ( 867) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 47 time to evaluate : 0.170 Fit side-chains revert: symmetry clash REVERT: A 78 ASN cc_start: 0.8359 (m110) cc_final: 0.8091 (m110) REVERT: A 329 PHE cc_start: 0.7802 (m-80) cc_final: 0.7494 (m-10) REVERT: A 459 PHE cc_start: 0.7605 (OUTLIER) cc_final: 0.6475 (t80) outliers start: 12 outliers final: 5 residues processed: 56 average time/residue: 0.3580 time to fit residues: 21.4343 Evaluate side-chains 52 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain A residue 459 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 38 optimal weight: 0.6980 chunk 36 optimal weight: 0.4980 chunk 40 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3725 r_free = 0.3725 target = 0.150872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.116989 restraints weight = 5278.433| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.00 r_work: 0.3190 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4539 Z= 0.139 Angle : 0.493 7.657 6192 Z= 0.259 Chirality : 0.039 0.150 691 Planarity : 0.004 0.053 751 Dihedral : 4.490 32.224 600 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.17 % Allowed : 19.96 % Favored : 77.87 % 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 (0.37), residues: 543 helix: 1.78 (0.27), residues: 386 sheet: None (None), residues: 0 loop : 0.54 (0.54), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 121 TYR 0.018 0.001 TYR A 84 PHE 0.010 0.001 PHE A 110 TRP 0.007 0.001 TRP A 553 HIS 0.002 0.000 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 4538) covalent geometry : angle 0.49304 ( 6190) SS BOND : bond 0.00241 ( 1) SS BOND : angle 0.72378 ( 2) hydrogen bonds : bond 0.04898 ( 302) hydrogen bonds : angle 4.73567 ( 867) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.190 Fit side-chains revert: symmetry clash REVERT: A 78 ASN cc_start: 0.8353 (m110) cc_final: 0.8041 (m110) REVERT: A 329 PHE cc_start: 0.7825 (m-80) cc_final: 0.7495 (m-10) REVERT: A 459 PHE cc_start: 0.7683 (OUTLIER) cc_final: 0.6591 (t80) outliers start: 10 outliers final: 5 residues processed: 53 average time/residue: 0.3321 time to fit residues: 18.9656 Evaluate side-chains 49 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain A residue 459 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 53 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 30 optimal weight: 0.0670 chunk 36 optimal weight: 0.3980 chunk 11 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 31 optimal weight: 0.0970 chunk 50 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 overall best weight: 0.3916 ------------------------------------------------------------------------------- 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 = 0.3765 r_free = 0.3765 target = 0.154790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.120961 restraints weight = 5229.035| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.03 r_work: 0.3243 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4539 Z= 0.110 Angle : 0.462 6.164 6192 Z= 0.243 Chirality : 0.038 0.135 691 Planarity : 0.004 0.052 751 Dihedral : 4.244 29.605 600 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.95 % Allowed : 20.61 % Favored : 77.44 % 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: 2.26 (0.37), residues: 543 helix: 1.94 (0.27), residues: 383 sheet: None (None), residues: 0 loop : 0.53 (0.54), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 121 TYR 0.014 0.001 TYR A 151 PHE 0.011 0.001 PHE A 110 TRP 0.010 0.001 TRP A 553 HIS 0.001 0.000 HIS A 372 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 4538) covalent geometry : angle 0.46155 ( 6190) SS BOND : bond 0.00193 ( 1) SS BOND : angle 0.59206 ( 2) hydrogen bonds : bond 0.04273 ( 302) hydrogen bonds : angle 4.56618 ( 867) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.177 Fit side-chains revert: symmetry clash REVERT: A 78 ASN cc_start: 0.8267 (m110) cc_final: 0.8045 (m110) REVERT: A 329 PHE cc_start: 0.7766 (m-80) cc_final: 0.7462 (m-10) REVERT: A 371 GLU cc_start: 0.7856 (tp30) cc_final: 0.7316 (tt0) REVERT: A 459 PHE cc_start: 0.7506 (OUTLIER) cc_final: 0.6390 (t80) outliers start: 9 outliers final: 6 residues processed: 55 average time/residue: 0.3317 time to fit residues: 19.5844 Evaluate side-chains 53 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 505 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 15 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 25 optimal weight: 0.0970 chunk 20 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 507 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.151664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.117989 restraints weight = 5279.646| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.99 r_work: 0.3198 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4539 Z= 0.133 Angle : 0.486 7.295 6192 Z= 0.255 Chirality : 0.039 0.150 691 Planarity : 0.004 0.052 751 Dihedral : 4.434 32.197 600 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.95 % Allowed : 20.82 % Favored : 77.22 % 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: 2.14 (0.37), residues: 543 helix: 1.82 (0.27), residues: 387 sheet: None (None), residues: 0 loop : 0.55 (0.54), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 121 TYR 0.017 0.001 TYR A 84 PHE 0.018 0.001 PHE A 164 TRP 0.008 0.001 TRP A 553 HIS 0.002 0.000 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 4538) covalent geometry : angle 0.48585 ( 6190) SS BOND : bond 0.00372 ( 1) SS BOND : angle 0.87061 ( 2) hydrogen bonds : bond 0.04706 ( 302) hydrogen bonds : angle 4.65114 ( 867) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.176 Fit side-chains REVERT: A 78 ASN cc_start: 0.8324 (m110) cc_final: 0.8039 (m110) REVERT: A 329 PHE cc_start: 0.7813 (m-80) cc_final: 0.7480 (m-10) REVERT: A 371 GLU cc_start: 0.7841 (tp30) cc_final: 0.7256 (tt0) REVERT: A 459 PHE cc_start: 0.7636 (OUTLIER) cc_final: 0.6551 (t80) outliers start: 9 outliers final: 5 residues processed: 52 average time/residue: 0.3797 time to fit residues: 21.0050 Evaluate side-chains 50 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain A residue 459 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 11 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 39 optimal weight: 0.0980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.152467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.118743 restraints weight = 5210.631| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.98 r_work: 0.3214 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4539 Z= 0.125 Angle : 0.476 6.784 6192 Z= 0.250 Chirality : 0.039 0.146 691 Planarity : 0.004 0.052 751 Dihedral : 4.376 31.562 600 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.52 % Allowed : 21.48 % Favored : 77.01 % 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 (0.37), residues: 543 helix: 1.85 (0.27), residues: 386 sheet: None (None), residues: 0 loop : 0.46 (0.54), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 121 TYR 0.016 0.001 TYR A 84 PHE 0.011 0.001 PHE A 110 TRP 0.009 0.001 TRP A 553 HIS 0.002 0.000 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 4538) covalent geometry : angle 0.47595 ( 6190) SS BOND : bond 0.00365 ( 1) SS BOND : angle 0.80346 ( 2) hydrogen bonds : bond 0.04589 ( 302) hydrogen bonds : angle 4.63375 ( 867) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.171 Fit side-chains REVERT: A 78 ASN cc_start: 0.8274 (m110) cc_final: 0.8006 (m110) REVERT: A 329 PHE cc_start: 0.7823 (m-80) cc_final: 0.7515 (m-10) REVERT: A 371 GLU cc_start: 0.7833 (tp30) cc_final: 0.7262 (tt0) REVERT: A 459 PHE cc_start: 0.7608 (OUTLIER) cc_final: 0.6536 (t80) outliers start: 7 outliers final: 5 residues processed: 48 average time/residue: 0.3451 time to fit residues: 17.7980 Evaluate side-chains 49 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain A residue 459 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 36 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 53 optimal weight: 8.9990 chunk 6 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3724 r_free = 0.3724 target = 0.150985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.117058 restraints weight = 5265.209| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 1.99 r_work: 0.3187 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4539 Z= 0.137 Angle : 0.492 7.449 6192 Z= 0.258 Chirality : 0.039 0.153 691 Planarity : 0.004 0.052 751 Dihedral : 4.476 33.441 600 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.95 % Allowed : 21.04 % Favored : 77.01 % 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: 2.06 (0.37), residues: 543 helix: 1.79 (0.27), residues: 387 sheet: None (None), residues: 0 loop : 0.46 (0.54), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 341 TYR 0.017 0.001 TYR A 84 PHE 0.019 0.001 PHE A 164 TRP 0.008 0.001 TRP A 235 HIS 0.002 0.000 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 4538) covalent geometry : angle 0.49187 ( 6190) SS BOND : bond 0.00362 ( 1) SS BOND : angle 0.79850 ( 2) hydrogen bonds : bond 0.04849 ( 302) hydrogen bonds : angle 4.69692 ( 867) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1614.89 seconds wall clock time: 28 minutes 24.18 seconds (1704.18 seconds total)