Starting phenix.real_space_refine on Thu Mar 6 01:12:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xb4_38210/03_2025/8xb4_38210.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xb4_38210/03_2025/8xb4_38210.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xb4_38210/03_2025/8xb4_38210.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xb4_38210/03_2025/8xb4_38210.map" model { file = "/net/cci-nas-00/data/ceres_data/8xb4_38210/03_2025/8xb4_38210.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xb4_38210/03_2025/8xb4_38210.cif" } resolution = 2.92 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.126 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 2894 2.51 5 N 665 2.21 5 O 728 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 4307 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4293 Classifications: {'peptide': 536} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 516} Chain breaks: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.21, per 1000 atoms: 0.75 Number of scatterers: 4307 At special positions: 0 Unit cell: (65.88, 66.96, 95.04, 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 728 8.00 N 665 7.00 C 2894 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 Links applied NAG-ASN " NAG A 701 " - " ASN A 184 " Time building additional restraints: 1.05 Conformation dependent library (CDL) restraints added in 521.4 milliseconds 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 988 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 0 sheets defined 81.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 66 through 74 removed outlier: 4.005A pdb=" N PHE A 72 " --> pdb=" O SER A 68 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N VAL A 74 " --> pdb=" O VAL A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 90 removed outlier: 3.525A pdb=" N VAL A 79 " --> pdb=" O ASP A 75 " (cutoff:3.500A) removed outlier: 4.215A 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 91 through 105 removed outlier: 3.652A pdb=" N LEU A 95 " --> pdb=" O GLY A 91 " (cutoff:3.500A) Proline residue: A 97 - end of helix Processing helix chain 'A' and resid 105 through 121 removed outlier: 3.524A pdb=" N LEU A 109 " --> pdb=" O ALA A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 130 removed outlier: 3.870A pdb=" N TRP A 128 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 3.713A 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 removed outlier: 3.805A pdb=" N GLY A 138 " --> pdb=" O PHE A 134 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N TYR A 151 " --> pdb=" O TYR A 147 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N VAL A 154 " --> pdb=" O PHE A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 207 removed outlier: 3.505A pdb=" N PHE A 207 " --> pdb=" O LYS A 204 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 204 through 207' Processing helix chain 'A' and resid 208 through 218 Processing helix chain 'A' and resid 220 through 224 Processing helix chain 'A' and resid 234 through 253 Processing helix chain 'A' and resid 264 through 283 Proline residue: A 270 - end of helix Processing helix chain 'A' and resid 286 through 296 removed outlier: 3.865A pdb=" N GLY A 290 " --> pdb=" O GLY A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 303 removed outlier: 3.788A pdb=" N LEU A 302 " --> pdb=" O ASP A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 320 Processing helix chain 'A' and resid 324 through 331 Processing helix chain 'A' and resid 338 through 372 Processing helix chain 'A' and resid 375 through 379 removed outlier: 3.542A pdb=" N VAL A 379 " --> pdb=" O ILE A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 396 Proline residue: A 392 - end of helix Processing helix chain 'A' and resid 400 through 435 Processing helix chain 'A' and resid 435 through 441 Processing helix chain 'A' and resid 441 through 456 Processing helix chain 'A' and resid 464 through 476 removed outlier: 3.731A pdb=" N VAL A 468 " --> pdb=" O GLY A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 494 Processing helix chain 'A' and resid 497 through 509 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: 4.293A pdb=" N SER A 565 " --> pdb=" O ILE A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 578 Processing helix chain 'A' and resid 583 through 593 Processing helix chain 'A' and resid 594 through 597 Processing helix chain 'A' and resid 598 through 603 removed outlier: 4.038A pdb=" N ALA A 602 " --> pdb=" O HIS A 598 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLN A 603 " --> pdb=" O HIS A 599 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 598 through 603' Processing helix chain 'A' and resid 610 through 615 removed outlier: 4.316A pdb=" N TRP A 614 " --> pdb=" O GLN A 610 " (cutoff:3.500A) 278 hydrogen bonds defined for protein. 819 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: 1.18 Time building geometry restraints manager: 1.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1257 1.34 - 1.46: 1195 1.46 - 1.58: 1964 1.58 - 1.70: 0 1.70 - 1.81: 31 Bond restraints: 4447 Sorted by residual: bond pdb=" C3 NAG A 701 " pdb=" O3 NAG A 701 " ideal model delta sigma weight residual 1.403 1.423 -0.020 2.00e-02 2.50e+03 9.86e-01 bond pdb=" C5 NAG A 701 " pdb=" O5 NAG A 701 " ideal model delta sigma weight residual 1.413 1.432 -0.019 2.00e-02 2.50e+03 9.34e-01 bond pdb=" CG LEU A 390 " pdb=" CD2 LEU A 390 " ideal model delta sigma weight residual 1.521 1.489 0.032 3.30e-02 9.18e+02 9.20e-01 bond pdb=" C PHE A 82 " pdb=" O PHE A 82 " ideal model delta sigma weight residual 1.244 1.235 0.008 9.80e-03 1.04e+04 6.95e-01 bond pdb=" CB VAL A 535 " pdb=" CG1 VAL A 535 " ideal model delta sigma weight residual 1.521 1.495 0.026 3.30e-02 9.18e+02 6.43e-01 ... (remaining 4442 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.18: 5756 1.18 - 2.36: 249 2.36 - 3.54: 45 3.54 - 4.72: 11 4.72 - 5.90: 8 Bond angle restraints: 6069 Sorted by residual: angle pdb=" N GLY A 478 " pdb=" CA GLY A 478 " pdb=" C GLY A 478 " ideal model delta sigma weight residual 113.18 107.55 5.63 2.37e+00 1.78e-01 5.64e+00 angle pdb=" C ASN A 596 " pdb=" N GLU A 597 " pdb=" CA GLU A 597 " ideal model delta sigma weight residual 123.17 120.08 3.09 1.49e+00 4.50e-01 4.30e+00 angle pdb=" CA TYR A 391 " pdb=" C TYR A 391 " pdb=" N PRO A 392 " ideal model delta sigma weight residual 118.44 121.69 -3.25 1.59e+00 3.96e-01 4.17e+00 angle pdb=" C VAL A 282 " pdb=" N THR A 283 " pdb=" CA THR A 283 " ideal model delta sigma weight residual 121.94 118.02 3.92 2.00e+00 2.50e-01 3.85e+00 angle pdb=" CA TYR A 111 " pdb=" CB TYR A 111 " pdb=" CG TYR A 111 " ideal model delta sigma weight residual 113.90 117.28 -3.38 1.80e+00 3.09e-01 3.53e+00 ... (remaining 6064 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.48: 2352 21.48 - 42.95: 121 42.95 - 64.43: 8 64.43 - 85.90: 7 85.90 - 107.38: 7 Dihedral angle restraints: 2495 sinusoidal: 944 harmonic: 1551 Sorted by residual: dihedral pdb=" CA THR A 544 " pdb=" C THR A 544 " pdb=" N TYR A 545 " pdb=" CA TYR A 545 " ideal model delta harmonic sigma weight residual 180.00 160.23 19.77 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" C2 NAG A 701 " pdb=" C3 NAG A 701 " pdb=" C4 NAG A 701 " pdb=" C5 NAG A 701 " ideal model delta sinusoidal sigma weight residual 53.78 -53.60 107.38 1 3.00e+01 1.11e-03 1.39e+01 dihedral pdb=" C2 NAG A 701 " pdb=" C3 NAG A 701 " pdb=" C4 NAG A 701 " pdb=" O4 NAG A 701 " ideal model delta sinusoidal sigma weight residual 175.11 68.05 107.06 1 3.00e+01 1.11e-03 1.38e+01 ... (remaining 2492 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 360 0.029 - 0.058: 208 0.058 - 0.087: 78 0.087 - 0.116: 27 0.116 - 0.145: 8 Chirality restraints: 681 Sorted by residual: chirality pdb=" C1 NAG A 701 " pdb=" ND2 ASN A 184 " pdb=" C2 NAG A 701 " pdb=" O5 NAG A 701 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-01 2.50e+01 5.25e-01 chirality pdb=" CA PRO A 132 " pdb=" N PRO A 132 " pdb=" C PRO A 132 " pdb=" CB PRO A 132 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.98e-01 chirality pdb=" CA ILE A 549 " pdb=" N ILE A 549 " pdb=" C ILE A 549 " pdb=" CB ILE A 549 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.85e-01 ... (remaining 678 not shown) Planarity restraints: 737 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 82 " -0.030 5.00e-02 4.00e+02 4.47e-02 3.20e+00 pdb=" N PRO A 83 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 83 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 83 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 111 " -0.014 2.00e-02 2.50e+03 1.23e-02 3.01e+00 pdb=" CG TYR A 111 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR A 111 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR A 111 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR A 111 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 111 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR A 111 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 111 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR A 391 " -0.029 5.00e-02 4.00e+02 4.31e-02 2.98e+00 pdb=" N PRO A 392 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 392 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 392 " -0.024 5.00e-02 4.00e+02 ... (remaining 734 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1130 2.79 - 3.32: 4134 3.32 - 3.84: 7479 3.84 - 4.37: 9160 4.37 - 4.90: 15607 Nonbonded interactions: 37510 Sorted by model distance: nonbonded pdb=" OH TYR A 496 " pdb=" OD2 ASP A 504 " model vdw 2.258 3.040 nonbonded pdb=" OE2 GLU A 425 " pdb=" OG1 THR A 429 " model vdw 2.279 3.040 nonbonded pdb=" NH1 ARG A 121 " pdb=" O ASN A 333 " model vdw 2.293 3.120 nonbonded pdb=" OD1 ASP A 75 " pdb=" OD1 ASN A 78 " model vdw 2.335 3.040 nonbonded pdb=" O ALA A 589 " pdb=" OG1 THR A 593 " model vdw 2.369 3.040 ... (remaining 37505 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: 0.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.060 Process input model: 14.840 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:10.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 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 : 0.005 0.038 4447 Z= 0.292 Angle : 0.606 5.903 6069 Z= 0.329 Chirality : 0.043 0.145 681 Planarity : 0.005 0.045 736 Dihedral : 14.468 107.378 1504 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.32), residues: 530 helix: -1.09 (0.23), residues: 379 sheet: None (None), residues: 0 loop : -1.19 (0.47), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 253 HIS 0.005 0.001 HIS A 280 PHE 0.012 0.001 PHE A 316 TYR 0.030 0.002 TYR A 111 ARG 0.003 0.000 ARG A 341 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.465 Fit side-chains REVERT: A 88 LYS cc_start: 0.8339 (tttp) cc_final: 0.8021 (ttmt) REVERT: A 206 LYS cc_start: 0.7992 (pttm) cc_final: 0.7682 (ptpt) REVERT: A 531 PHE cc_start: 0.7634 (t80) cc_final: 0.7178 (t80) outliers start: 0 outliers final: 1 residues processed: 75 average time/residue: 0.6713 time to fit residues: 53.6229 Evaluate side-chains 54 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 53 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 44 optimal weight: 0.5980 chunk 40 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 13 optimal weight: 0.0970 chunk 27 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 HIS A 610 GLN A 613 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.134281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.113749 restraints weight = 4941.611| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.49 r_work: 0.3177 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4447 Z= 0.205 Angle : 0.559 6.841 6069 Z= 0.285 Chirality : 0.042 0.173 681 Planarity : 0.005 0.044 736 Dihedral : 5.985 31.440 600 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.55 % Allowed : 9.07 % Favored : 89.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.35), residues: 530 helix: 0.09 (0.25), residues: 384 sheet: None (None), residues: 0 loop : -0.39 (0.53), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 553 HIS 0.003 0.001 HIS A 222 PHE 0.012 0.001 PHE A 409 TYR 0.019 0.002 TYR A 111 ARG 0.001 0.000 ARG A 604 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.635 Fit side-chains REVERT: A 206 LYS cc_start: 0.8181 (pttm) cc_final: 0.7662 (ptpt) outliers start: 7 outliers final: 1 residues processed: 68 average time/residue: 1.0318 time to fit residues: 74.0126 Evaluate side-chains 56 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 55 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 2 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 4 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 610 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.133107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.113240 restraints weight = 4954.843| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 1.40 r_work: 0.3169 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4447 Z= 0.259 Angle : 0.556 6.092 6069 Z= 0.286 Chirality : 0.042 0.152 681 Planarity : 0.005 0.046 736 Dihedral : 4.795 32.002 600 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.99 % Allowed : 11.50 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.36), residues: 530 helix: 0.49 (0.26), residues: 385 sheet: None (None), residues: 0 loop : -0.31 (0.53), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 553 HIS 0.003 0.001 HIS A 280 PHE 0.013 0.001 PHE A 316 TYR 0.020 0.002 TYR A 111 ARG 0.002 0.000 ARG A 341 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.480 Fit side-chains REVERT: A 206 LYS cc_start: 0.8328 (pttm) cc_final: 0.7825 (ptpt) outliers start: 9 outliers final: 1 residues processed: 64 average time/residue: 1.4719 time to fit residues: 97.9111 Evaluate side-chains 54 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 53 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 24 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 25 optimal weight: 0.0000 chunk 32 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 30 optimal weight: 0.3980 chunk 51 optimal weight: 0.0040 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 610 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.135754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.115362 restraints weight = 4976.360| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.50 r_work: 0.3194 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4447 Z= 0.161 Angle : 0.498 6.061 6069 Z= 0.255 Chirality : 0.039 0.135 681 Planarity : 0.004 0.044 736 Dihedral : 4.176 20.248 598 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.99 % Allowed : 12.39 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.37), residues: 530 helix: 0.91 (0.26), residues: 386 sheet: None (None), residues: 0 loop : -0.15 (0.53), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 553 HIS 0.002 0.001 HIS A 220 PHE 0.011 0.001 PHE A 110 TYR 0.014 0.001 TYR A 84 ARG 0.001 0.000 ARG A 442 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.447 Fit side-chains REVERT: A 206 LYS cc_start: 0.8225 (pttm) cc_final: 0.7641 (ptpt) REVERT: A 310 ASP cc_start: 0.8384 (m-30) cc_final: 0.8180 (m-30) REVERT: A 556 TRP cc_start: 0.7378 (m-10) cc_final: 0.7116 (m-10) outliers start: 9 outliers final: 4 residues processed: 66 average time/residue: 0.6572 time to fit residues: 46.6571 Evaluate side-chains 57 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 418 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 26 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 43 optimal weight: 0.4980 chunk 16 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 42 optimal weight: 0.3980 chunk 10 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 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 610 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.133870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.113954 restraints weight = 5029.438| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.43 r_work: 0.3184 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4447 Z= 0.210 Angle : 0.523 5.880 6069 Z= 0.268 Chirality : 0.040 0.145 681 Planarity : 0.004 0.045 736 Dihedral : 4.247 20.616 598 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.65 % Allowed : 13.27 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.36), residues: 530 helix: 0.97 (0.26), residues: 385 sheet: None (None), residues: 0 loop : -0.07 (0.53), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 553 HIS 0.002 0.001 HIS A 280 PHE 0.012 0.001 PHE A 408 TYR 0.016 0.001 TYR A 84 ARG 0.001 0.000 ARG A 604 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.456 Fit side-chains REVERT: A 206 LYS cc_start: 0.8451 (pttm) cc_final: 0.7905 (ptpt) outliers start: 12 outliers final: 6 residues processed: 63 average time/residue: 0.6616 time to fit residues: 44.6161 Evaluate side-chains 60 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 235 TRP Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 418 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 12 optimal weight: 7.9990 chunk 4 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 610 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.131866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.111233 restraints weight = 4950.197| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 1.49 r_work: 0.3154 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4447 Z= 0.256 Angle : 0.547 6.245 6069 Z= 0.281 Chirality : 0.042 0.145 681 Planarity : 0.004 0.047 736 Dihedral : 4.397 21.516 598 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.65 % Allowed : 13.72 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.36), residues: 530 helix: 0.91 (0.26), residues: 385 sheet: None (None), residues: 0 loop : -0.03 (0.53), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 553 HIS 0.003 0.001 HIS A 280 PHE 0.013 0.001 PHE A 316 TYR 0.018 0.002 TYR A 84 ARG 0.002 0.000 ARG A 604 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.403 Fit side-chains REVERT: A 206 LYS cc_start: 0.8356 (pttm) cc_final: 0.7774 (ptpt) REVERT: A 373 LYS cc_start: 0.7714 (mmmt) cc_final: 0.7307 (mmtp) outliers start: 12 outliers final: 6 residues processed: 61 average time/residue: 0.6929 time to fit residues: 45.1709 Evaluate side-chains 58 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 235 TRP Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 418 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 42 optimal weight: 0.4980 chunk 38 optimal weight: 0.5980 chunk 47 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 chunk 35 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 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 610 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.133157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.112753 restraints weight = 4959.167| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 1.46 r_work: 0.3116 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4447 Z= 0.214 Angle : 0.521 6.238 6069 Z= 0.267 Chirality : 0.040 0.145 681 Planarity : 0.004 0.046 736 Dihedral : 4.288 20.010 598 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.43 % Allowed : 14.82 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.36), residues: 530 helix: 1.02 (0.26), residues: 385 sheet: None (None), residues: 0 loop : -0.00 (0.53), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 553 HIS 0.003 0.001 HIS A 280 PHE 0.016 0.001 PHE A 408 TYR 0.016 0.001 TYR A 84 ARG 0.001 0.000 ARG A 604 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.418 Fit side-chains REVERT: A 373 LYS cc_start: 0.7753 (mmmt) cc_final: 0.7263 (mmtp) REVERT: A 596 ASN cc_start: 0.6969 (p0) cc_final: 0.6703 (p0) outliers start: 11 outliers final: 7 residues processed: 64 average time/residue: 0.6231 time to fit residues: 42.7102 Evaluate side-chains 62 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 235 TRP Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 508 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 35 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 43 optimal weight: 0.4980 chunk 17 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 31 optimal weight: 0.2980 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 610 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.133921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.114069 restraints weight = 4900.910| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.41 r_work: 0.3163 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4447 Z= 0.210 Angle : 0.527 6.162 6069 Z= 0.270 Chirality : 0.040 0.146 681 Planarity : 0.004 0.046 736 Dihedral : 4.273 19.287 598 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.43 % Allowed : 14.38 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.37), residues: 530 helix: 1.05 (0.26), residues: 386 sheet: None (None), residues: 0 loop : 0.02 (0.54), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 553 HIS 0.003 0.001 HIS A 280 PHE 0.014 0.001 PHE A 275 TYR 0.016 0.001 TYR A 84 ARG 0.001 0.000 ARG A 604 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.424 Fit side-chains REVERT: A 373 LYS cc_start: 0.7616 (mmmt) cc_final: 0.7147 (mmtp) REVERT: A 596 ASN cc_start: 0.6950 (p0) cc_final: 0.6706 (p0) outliers start: 11 outliers final: 8 residues processed: 61 average time/residue: 0.6427 time to fit residues: 41.9637 Evaluate side-chains 64 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 235 TRP Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 508 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 31 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 46 optimal weight: 0.2980 chunk 8 optimal weight: 0.5980 chunk 47 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 43 optimal weight: 0.0870 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 610 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.144493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.122856 restraints weight = 4910.535| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 1.73 r_work: 0.3213 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4447 Z= 0.175 Angle : 0.508 5.980 6069 Z= 0.261 Chirality : 0.040 0.167 681 Planarity : 0.004 0.046 736 Dihedral : 4.033 15.434 598 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.21 % Allowed : 15.93 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.37), residues: 530 helix: 1.18 (0.26), residues: 386 sheet: None (None), residues: 0 loop : 0.07 (0.54), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 553 HIS 0.002 0.000 HIS A 280 PHE 0.014 0.001 PHE A 275 TYR 0.015 0.001 TYR A 84 ARG 0.001 0.000 ARG A 604 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.425 Fit side-chains REVERT: A 373 LYS cc_start: 0.7771 (mmmt) cc_final: 0.7330 (mmtp) REVERT: A 580 THR cc_start: 0.8096 (m) cc_final: 0.7486 (p) REVERT: A 596 ASN cc_start: 0.6916 (p0) cc_final: 0.6626 (p0) outliers start: 10 outliers final: 6 residues processed: 61 average time/residue: 0.7548 time to fit residues: 49.2659 Evaluate side-chains 58 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 235 TRP Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 418 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 16 optimal weight: 0.5980 chunk 23 optimal weight: 0.2980 chunk 8 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 21 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 610 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.143270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.121662 restraints weight = 4843.479| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.72 r_work: 0.3172 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4447 Z= 0.205 Angle : 0.528 6.220 6069 Z= 0.271 Chirality : 0.041 0.160 681 Planarity : 0.004 0.046 736 Dihedral : 4.143 16.099 598 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.77 % Allowed : 16.81 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.37), residues: 530 helix: 1.12 (0.26), residues: 388 sheet: None (None), residues: 0 loop : 0.04 (0.55), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 553 HIS 0.002 0.001 HIS A 280 PHE 0.015 0.001 PHE A 275 TYR 0.016 0.001 TYR A 84 ARG 0.001 0.000 ARG A 604 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.404 Fit side-chains REVERT: A 373 LYS cc_start: 0.7770 (mmmt) cc_final: 0.7333 (mmtp) REVERT: A 580 THR cc_start: 0.8073 (m) cc_final: 0.7461 (p) REVERT: A 596 ASN cc_start: 0.6876 (p0) cc_final: 0.6573 (p0) outliers start: 8 outliers final: 7 residues processed: 56 average time/residue: 0.5892 time to fit residues: 35.6112 Evaluate side-chains 59 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 235 TRP Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 508 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 4 optimal weight: 0.5980 chunk 50 optimal weight: 0.0020 chunk 29 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 13 optimal weight: 6.9990 chunk 44 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 610 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.143581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.121934 restraints weight = 4834.357| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.72 r_work: 0.3176 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4447 Z= 0.196 Angle : 0.521 6.243 6069 Z= 0.267 Chirality : 0.040 0.164 681 Planarity : 0.004 0.047 736 Dihedral : 4.110 15.928 598 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.77 % Allowed : 17.04 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.37), residues: 530 helix: 1.13 (0.26), residues: 388 sheet: None (None), residues: 0 loop : 0.06 (0.55), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 553 HIS 0.002 0.000 HIS A 280 PHE 0.015 0.001 PHE A 275 TYR 0.016 0.001 TYR A 84 ARG 0.001 0.000 ARG A 604 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2871.09 seconds wall clock time: 51 minutes 28.16 seconds (3088.16 seconds total)