Starting phenix.real_space_refine on Wed Mar 5 17:59:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bg6_16024/03_2025/8bg6_16024.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bg6_16024/03_2025/8bg6_16024.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8bg6_16024/03_2025/8bg6_16024.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bg6_16024/03_2025/8bg6_16024.map" model { file = "/net/cci-nas-00/data/ceres_data/8bg6_16024/03_2025/8bg6_16024.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bg6_16024/03_2025/8bg6_16024.cif" } resolution = 4.11 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 ------------------------------------------------------------------------------- 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= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 16 5.16 5 C 1981 2.51 5 N 527 2.21 5 O 600 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 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: 3124 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 845 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 105} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 815 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 1450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1450 Classifications: {'peptide': 182} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 172} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" 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: 2.63, per 1000 atoms: 0.84 Number of scatterers: 3124 At special positions: 0 Unit cell: (66.64, 65.96, 94.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 16 16.00 O 600 8.00 N 527 7.00 C 1981 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 95 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=1.94 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " 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 E2000 " - " ASN E 343 " Time building additional restraints: 0.73 Conformation dependent library (CDL) restraints added in 382.0 milliseconds 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 728 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 7 sheets defined 8.3% alpha, 27.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 86 through 90 removed outlier: 3.596A pdb=" N THR A 90 " --> pdb=" O PRO A 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 342 removed outlier: 3.781A pdb=" N VAL E 341 " --> pdb=" O PRO E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 349 through 353 removed outlier: 3.681A pdb=" N ALA E 352 " --> pdb=" O SER E 349 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N TRP E 353 " --> pdb=" O VAL E 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 349 through 353' Processing helix chain 'E' and resid 384 through 388 removed outlier: 3.579A pdb=" N LEU E 387 " --> pdb=" O PRO E 384 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ASN E 388 " --> pdb=" O THR E 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 384 through 388' Processing helix chain 'E' and resid 404 through 410 removed outlier: 3.683A pdb=" N VAL E 407 " --> pdb=" O GLY E 404 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 502 through 506 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 7 removed outlier: 3.583A pdb=" N SER A 21 " --> pdb=" O SER A 7 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 11 removed outlier: 6.072A pdb=" N GLY A 10 " --> pdb=" O THR A 111 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL A 37 " --> pdb=" O TYR A 94 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N ARG A 38 " --> pdb=" O TRP A 47 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N TRP A 47 " --> pdb=" O ARG A 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.524A pdb=" N LEU B 11 " --> pdb=" O GLU B 105 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N GLN B 37 " --> pdb=" O LEU B 46 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N LEU B 46 " --> pdb=" O GLN B 37 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TYR B 49 " --> pdb=" O HIS B 53 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N HIS B 53 " --> pdb=" O TYR B 49 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 19 through 24 Processing sheet with id=AA5, first strand: chain 'E' and resid 355 through 358 removed outlier: 7.161A pdb=" N ASN E 437 " --> pdb=" O PHE E 374 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N PHE E 374 " --> pdb=" O ASN E 437 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 452 through 453 Processing sheet with id=AA7, first strand: chain 'E' and resid 473 through 474 removed outlier: 3.500A pdb=" N TYR E 473 " --> pdb=" O TYR E 489 " (cutoff:3.500A) 85 hydrogen bonds defined for protein. 198 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: 0.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 757 1.33 - 1.45: 729 1.45 - 1.57: 1696 1.57 - 1.69: 0 1.69 - 1.82: 20 Bond restraints: 3202 Sorted by residual: bond pdb=" N SER A 31 " pdb=" CA SER A 31 " ideal model delta sigma weight residual 1.458 1.485 -0.026 9.00e-03 1.23e+04 8.67e+00 bond pdb=" N ASN E 343 " pdb=" CA ASN E 343 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.06e-02 8.90e+03 8.49e+00 bond pdb=" N GLU A 26 " pdb=" CA GLU A 26 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.23e-02 6.61e+03 8.41e+00 bond pdb=" N VAL E 362 " pdb=" CA VAL E 362 " ideal model delta sigma weight residual 1.459 1.492 -0.034 1.19e-02 7.06e+03 8.09e+00 bond pdb=" N TYR A 93 " pdb=" CA TYR A 93 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.16e-02 7.43e+03 7.95e+00 ... (remaining 3197 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 4044 1.73 - 3.46: 254 3.46 - 5.19: 44 5.19 - 6.93: 7 6.93 - 8.66: 3 Bond angle restraints: 4352 Sorted by residual: angle pdb=" CB LYS E 386 " pdb=" CG LYS E 386 " pdb=" CD LYS E 386 " ideal model delta sigma weight residual 111.30 119.96 -8.66 2.30e+00 1.89e-01 1.42e+01 angle pdb=" CA THR A 108 " pdb=" C THR A 108 " pdb=" O THR A 108 " ideal model delta sigma weight residual 121.46 117.15 4.31 1.17e+00 7.31e-01 1.36e+01 angle pdb=" CA ILE A 103 " pdb=" C ILE A 103 " pdb=" O ILE A 103 " ideal model delta sigma weight residual 120.25 116.69 3.56 9.90e-01 1.02e+00 1.29e+01 angle pdb=" C ILE A 103 " pdb=" N TRP A 104 " pdb=" CA TRP A 104 " ideal model delta sigma weight residual 123.00 127.93 -4.93 1.38e+00 5.25e-01 1.28e+01 angle pdb=" CA GLN E 474 " pdb=" CB GLN E 474 " pdb=" CG GLN E 474 " ideal model delta sigma weight residual 114.10 121.07 -6.97 2.00e+00 2.50e-01 1.21e+01 ... (remaining 4347 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.98: 1706 15.98 - 31.95: 144 31.95 - 47.93: 39 47.93 - 63.91: 5 63.91 - 79.88: 2 Dihedral angle restraints: 1896 sinusoidal: 746 harmonic: 1150 Sorted by residual: dihedral pdb=" CB CYS E 480 " pdb=" SG CYS E 480 " pdb=" SG CYS E 488 " pdb=" CB CYS E 488 " ideal model delta sinusoidal sigma weight residual 93.00 161.54 -68.54 1 1.00e+01 1.00e-02 6.09e+01 dihedral pdb=" CA GLY A 105 " pdb=" C GLY A 105 " pdb=" N GLN A 106 " pdb=" CA GLN A 106 " ideal model delta harmonic sigma weight residual -180.00 -161.50 -18.50 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" C SER A 31 " pdb=" N SER A 31 " pdb=" CA SER A 31 " pdb=" CB SER A 31 " ideal model delta harmonic sigma weight residual -122.60 -131.69 9.09 0 2.50e+00 1.60e-01 1.32e+01 ... (remaining 1893 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 377 0.068 - 0.136: 75 0.136 - 0.204: 15 0.204 - 0.272: 0 0.272 - 0.340: 2 Chirality restraints: 469 Sorted by residual: chirality pdb=" CA ILE A 103 " pdb=" N ILE A 103 " pdb=" C ILE A 103 " pdb=" CB ILE A 103 " both_signs ideal model delta sigma weight residual False 2.43 2.77 -0.34 2.00e-01 2.50e+01 2.89e+00 chirality pdb=" CA SER A 31 " pdb=" N SER A 31 " pdb=" C SER A 31 " pdb=" CB SER A 31 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.33 2.00e-01 2.50e+01 2.65e+00 chirality pdb=" CA ASN A 76 " pdb=" N ASN A 76 " pdb=" C ASN A 76 " pdb=" CB ASN A 76 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.86e-01 ... (remaining 466 not shown) Planarity restraints: 566 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 40 " -0.042 5.00e-02 4.00e+02 6.32e-02 6.40e+00 pdb=" N PRO A 41 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO A 41 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 41 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 96 " 0.011 2.00e-02 2.50e+03 2.27e-02 5.16e+00 pdb=" C ALA A 96 " -0.039 2.00e-02 2.50e+03 pdb=" O ALA A 96 " 0.015 2.00e-02 2.50e+03 pdb=" N ARG A 97 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 16 " -0.009 2.00e-02 2.50e+03 1.90e-02 3.62e+00 pdb=" C GLY A 16 " 0.033 2.00e-02 2.50e+03 pdb=" O GLY A 16 " -0.012 2.00e-02 2.50e+03 pdb=" N SER A 17 " -0.011 2.00e-02 2.50e+03 ... (remaining 563 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 1161 2.86 - 3.37: 2456 3.37 - 3.88: 4514 3.88 - 4.39: 4882 4.39 - 4.90: 8948 Nonbonded interactions: 21961 Sorted by model distance: nonbonded pdb=" O ASP B 28 " pdb=" OD1 ASP B 28 " model vdw 2.348 3.040 nonbonded pdb=" O MET A 99 " pdb=" CG ARG A 100 " model vdw 2.425 3.440 nonbonded pdb=" OE1 GLU A 102 " pdb=" OH TYR B 36 " model vdw 2.463 3.040 nonbonded pdb=" OD1 ASN E 448 " pdb=" N ASN E 450 " model vdw 2.473 3.120 nonbonded pdb=" O SER E 366 " pdb=" N TYR E 369 " model vdw 2.496 3.120 ... (remaining 21956 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.420 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: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.290 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 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 : 0.006 0.042 3202 Z= 0.400 Angle : 0.937 8.657 4352 Z= 0.604 Chirality : 0.060 0.340 469 Planarity : 0.005 0.068 565 Dihedral : 12.582 79.885 1156 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 0.00 % Allowed : 9.14 % Favored : 90.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.90 (0.43), residues: 392 helix: -3.56 (0.97), residues: 18 sheet: 0.73 (0.50), residues: 116 loop : -1.06 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 436 HIS 0.006 0.002 HIS B 90 PHE 0.011 0.001 PHE E 400 TYR 0.014 0.001 TYR E 473 ARG 0.002 0.000 ARG B 61 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.1564 time to fit residues: 15.2888 Evaluate side-chains 61 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 16 optimal weight: 0.0470 chunk 10 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 11 optimal weight: 0.3980 chunk 18 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 HIS B 34 ASN ** E 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.144183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.120520 restraints weight = 4366.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.118731 restraints weight = 5780.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.116545 restraints weight = 5979.820| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3202 Z= 0.169 Angle : 0.565 5.110 4352 Z= 0.301 Chirality : 0.045 0.136 469 Planarity : 0.004 0.035 565 Dihedral : 4.069 14.608 461 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.35 (0.44), residues: 392 helix: -3.43 (0.95), residues: 18 sheet: 0.62 (0.50), residues: 127 loop : -0.41 (0.41), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 436 HIS 0.003 0.001 HIS B 90 PHE 0.010 0.001 PHE E 490 TYR 0.014 0.001 TYR E 453 ARG 0.004 0.000 ARG E 509 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 ASP cc_start: 0.8286 (t0) cc_final: 0.8078 (t0) REVERT: A 88 GLU cc_start: 0.7391 (tp30) cc_final: 0.7063 (tp30) REVERT: E 370 ASN cc_start: 0.7915 (p0) cc_final: 0.7695 (p0) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.1653 time to fit residues: 16.2971 Evaluate side-chains 64 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 31 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 29 optimal weight: 0.0060 chunk 4 optimal weight: 0.8980 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.146499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.135525 restraints weight = 4299.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.128448 restraints weight = 8092.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.122979 restraints weight = 8153.410| |-----------------------------------------------------------------------------| r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3202 Z= 0.160 Angle : 0.530 4.923 4352 Z= 0.283 Chirality : 0.044 0.131 469 Planarity : 0.004 0.036 565 Dihedral : 3.918 13.826 461 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.18 (0.44), residues: 392 helix: -3.34 (0.98), residues: 18 sheet: 0.59 (0.50), residues: 129 loop : -0.20 (0.41), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 436 HIS 0.003 0.001 HIS B 90 PHE 0.011 0.001 PHE B 73 TYR 0.010 0.001 TYR B 49 ARG 0.002 0.000 ARG A 66 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.358 Fit side-chains revert: symmetry clash REVERT: A 72 ASP cc_start: 0.8297 (t0) cc_final: 0.7997 (t0) REVERT: A 88 GLU cc_start: 0.7318 (tp30) cc_final: 0.7054 (tp30) REVERT: E 370 ASN cc_start: 0.8014 (p0) cc_final: 0.7751 (p0) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1524 time to fit residues: 15.2097 Evaluate side-chains 73 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 36 optimal weight: 0.0980 chunk 27 optimal weight: 0.7980 chunk 21 optimal weight: 0.0470 chunk 8 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 24 optimal weight: 10.0000 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.148965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.138131 restraints weight = 4332.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.129654 restraints weight = 7302.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.125442 restraints weight = 5340.110| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.3162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3202 Z= 0.135 Angle : 0.519 5.356 4352 Z= 0.275 Chirality : 0.044 0.173 469 Planarity : 0.004 0.041 565 Dihedral : 3.854 13.002 461 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.01 (0.44), residues: 392 helix: -3.07 (0.93), residues: 24 sheet: 0.76 (0.50), residues: 126 loop : -0.02 (0.41), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 36 HIS 0.003 0.001 HIS B 90 PHE 0.010 0.001 PHE B 73 TYR 0.008 0.001 TYR E 453 ARG 0.004 0.000 ARG E 357 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.318 Fit side-chains revert: symmetry clash REVERT: A 31 SER cc_start: 0.9263 (m) cc_final: 0.8706 (t) REVERT: A 72 ASP cc_start: 0.8421 (t0) cc_final: 0.8055 (t0) REVERT: B 79 GLN cc_start: 0.8678 (mp10) cc_final: 0.8456 (mp10) REVERT: B 91 CYS cc_start: 0.8722 (t) cc_final: 0.8489 (p) REVERT: E 370 ASN cc_start: 0.8334 (p0) cc_final: 0.8083 (p0) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.1424 time to fit residues: 14.7516 Evaluate side-chains 72 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 11 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 26 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 17 optimal weight: 6.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 = 0.3395 r_free = 0.3395 target = 0.130923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.117146 restraints weight = 4569.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.110257 restraints weight = 10032.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.105941 restraints weight = 8006.206| |-----------------------------------------------------------------------------| r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 3202 Z= 0.475 Angle : 0.702 6.222 4352 Z= 0.380 Chirality : 0.049 0.147 469 Planarity : 0.005 0.039 565 Dihedral : 4.754 17.803 461 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 0.29 % Allowed : 2.95 % Favored : 96.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.49 (0.43), residues: 392 helix: -3.04 (0.79), residues: 30 sheet: 0.43 (0.45), residues: 144 loop : -0.37 (0.42), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.004 TRP A 36 HIS 0.009 0.002 HIS B 53 PHE 0.014 0.002 PHE A 67 TYR 0.019 0.003 TYR B 49 ARG 0.004 0.001 ARG E 457 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 75 time to evaluate : 0.360 Fit side-chains revert: symmetry clash REVERT: E 370 ASN cc_start: 0.8036 (p0) cc_final: 0.7765 (p0) REVERT: E 474 GLN cc_start: 0.7756 (pp30) cc_final: 0.7518 (pp30) outliers start: 1 outliers final: 1 residues processed: 76 average time/residue: 0.1661 time to fit residues: 15.1371 Evaluate side-chains 68 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 67 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 1 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.138927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.127659 restraints weight = 4430.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.120757 restraints weight = 8312.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.116777 restraints weight = 6769.323| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3202 Z= 0.166 Angle : 0.558 5.445 4352 Z= 0.296 Chirality : 0.045 0.134 469 Planarity : 0.004 0.047 565 Dihedral : 4.103 14.857 461 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.18 (0.44), residues: 392 helix: -3.22 (0.88), residues: 24 sheet: 0.50 (0.45), residues: 152 loop : -0.10 (0.43), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 36 HIS 0.005 0.001 HIS B 90 PHE 0.012 0.001 PHE B 73 TYR 0.009 0.001 TYR B 36 ARG 0.003 0.001 ARG E 357 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.360 Fit side-chains revert: symmetry clash REVERT: A 81 GLN cc_start: 0.8038 (mm110) cc_final: 0.7706 (mm-40) REVERT: E 370 ASN cc_start: 0.7771 (p0) cc_final: 0.7497 (p0) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.1823 time to fit residues: 17.4835 Evaluate side-chains 68 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 7.9990 chunk 35 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 13 optimal weight: 7.9990 chunk 27 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 20 optimal weight: 0.0980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.143709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.131849 restraints weight = 4456.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.124798 restraints weight = 8316.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.119525 restraints weight = 7361.453| |-----------------------------------------------------------------------------| r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.3529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3202 Z= 0.168 Angle : 0.542 4.323 4352 Z= 0.287 Chirality : 0.044 0.134 469 Planarity : 0.004 0.046 565 Dihedral : 3.917 14.429 461 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.05 (0.44), residues: 392 helix: -3.24 (0.88), residues: 24 sheet: 0.73 (0.46), residues: 143 loop : -0.10 (0.42), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 436 HIS 0.003 0.001 HIS B 90 PHE 0.011 0.001 PHE B 73 TYR 0.008 0.001 TYR E 453 ARG 0.002 0.000 ARG A 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.291 Fit side-chains revert: symmetry clash REVERT: A 72 ASP cc_start: 0.8169 (t0) cc_final: 0.7909 (t0) REVERT: B 91 CYS cc_start: 0.8842 (t) cc_final: 0.8166 (p) REVERT: E 370 ASN cc_start: 0.8054 (p0) cc_final: 0.7799 (p0) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.1790 time to fit residues: 16.3465 Evaluate side-chains 63 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 20 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 31 optimal weight: 0.7980 chunk 26 optimal weight: 40.0000 chunk 11 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 28 optimal weight: 0.4980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3476 r_free = 0.3476 target = 0.138149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.109949 restraints weight = 4380.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.109460 restraints weight = 4559.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.109448 restraints weight = 4753.226| |-----------------------------------------------------------------------------| r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.3643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3202 Z= 0.184 Angle : 0.564 4.340 4352 Z= 0.299 Chirality : 0.044 0.132 469 Planarity : 0.004 0.048 565 Dihedral : 3.893 13.553 461 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.02 (0.44), residues: 392 helix: -3.25 (0.88), residues: 24 sheet: 0.63 (0.45), residues: 152 loop : 0.00 (0.44), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 36 HIS 0.003 0.001 HIS B 90 PHE 0.011 0.001 PHE B 73 TYR 0.009 0.001 TYR B 36 ARG 0.004 0.000 ARG E 357 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: A 72 ASP cc_start: 0.8285 (t0) cc_final: 0.7997 (t0) REVERT: B 91 CYS cc_start: 0.8896 (t) cc_final: 0.8414 (p) REVERT: E 370 ASN cc_start: 0.8251 (p0) cc_final: 0.8038 (p0) REVERT: E 474 GLN cc_start: 0.7773 (pp30) cc_final: 0.7413 (pp30) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1624 time to fit residues: 15.8382 Evaluate side-chains 64 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 14 optimal weight: 0.0050 chunk 32 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 28 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 35 optimal weight: 30.0000 chunk 25 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 overall best weight: 1.0796 ------------------------------------------------------------------------------- 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 = 0.3467 r_free = 0.3467 target = 0.136984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.115120 restraints weight = 4484.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.111160 restraints weight = 9002.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.110951 restraints weight = 9619.037| |-----------------------------------------------------------------------------| r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3202 Z= 0.223 Angle : 0.589 5.172 4352 Z= 0.313 Chirality : 0.045 0.148 469 Planarity : 0.004 0.048 565 Dihedral : 4.019 14.057 461 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.11 (0.44), residues: 392 helix: -3.21 (0.88), residues: 24 sheet: 0.54 (0.44), residues: 154 loop : -0.05 (0.44), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 436 HIS 0.002 0.001 HIS B 90 PHE 0.011 0.001 PHE B 73 TYR 0.011 0.001 TYR B 36 ARG 0.003 0.000 ARG E 357 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.402 Fit side-chains revert: symmetry clash REVERT: A 31 SER cc_start: 0.9196 (m) cc_final: 0.8644 (t) REVERT: A 72 ASP cc_start: 0.8344 (t0) cc_final: 0.8057 (t0) REVERT: B 91 CYS cc_start: 0.8915 (t) cc_final: 0.8435 (p) REVERT: E 370 ASN cc_start: 0.7510 (p0) cc_final: 0.7242 (p0) REVERT: E 474 GLN cc_start: 0.7779 (pp30) cc_final: 0.7563 (pp30) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.1579 time to fit residues: 14.1139 Evaluate side-chains 62 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 37 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 1 optimal weight: 0.0870 chunk 21 optimal weight: 0.3980 chunk 8 optimal weight: 0.0060 chunk 3 optimal weight: 0.3980 chunk 16 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 35 optimal weight: 20.0000 overall best weight: 0.3374 ------------------------------------------------------------------------------- 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 = 0.3545 r_free = 0.3545 target = 0.143401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.131525 restraints weight = 4345.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.130651 restraints weight = 7456.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.128992 restraints weight = 8037.347| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.3816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3202 Z= 0.155 Angle : 0.557 4.884 4352 Z= 0.292 Chirality : 0.044 0.137 469 Planarity : 0.004 0.052 565 Dihedral : 3.838 13.606 461 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.07 (0.44), residues: 392 helix: -3.24 (0.84), residues: 24 sheet: 0.84 (0.47), residues: 143 loop : -0.03 (0.43), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 436 HIS 0.004 0.001 HIS B 90 PHE 0.011 0.001 PHE B 73 TYR 0.010 0.001 TYR B 36 ARG 0.004 0.000 ARG E 357 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.368 Fit side-chains revert: symmetry clash REVERT: A 72 ASP cc_start: 0.8125 (t0) cc_final: 0.7863 (t0) REVERT: B 91 CYS cc_start: 0.8846 (t) cc_final: 0.8275 (p) REVERT: E 400 PHE cc_start: 0.7529 (m-80) cc_final: 0.7226 (m-80) REVERT: E 503 VAL cc_start: 0.8477 (t) cc_final: 0.8177 (t) REVERT: E 506 GLN cc_start: 0.8859 (mp-120) cc_final: 0.8253 (mp10) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.1842 time to fit residues: 17.6974 Evaluate side-chains 64 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 36 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 chunk 15 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 21 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3481 r_free = 0.3481 target = 0.138372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.127122 restraints weight = 4372.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.119943 restraints weight = 9029.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.114263 restraints weight = 7384.907| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.3765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3202 Z= 0.203 Angle : 0.577 4.957 4352 Z= 0.306 Chirality : 0.045 0.145 469 Planarity : 0.004 0.049 565 Dihedral : 3.942 13.898 461 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.01 (0.44), residues: 392 helix: -3.33 (0.82), residues: 24 sheet: 0.78 (0.46), residues: 145 loop : -0.05 (0.43), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 436 HIS 0.002 0.001 HIS B 90 PHE 0.011 0.001 PHE B 73 TYR 0.010 0.001 TYR B 96 ARG 0.004 0.000 ARG E 357 =============================================================================== Job complete usr+sys time: 1557.09 seconds wall clock time: 27 minutes 35.71 seconds (1655.71 seconds total)