Starting phenix.real_space_refine on Wed Mar 5 17:07:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y7k_33668/03_2025/7y7k_33668.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y7k_33668/03_2025/7y7k_33668.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y7k_33668/03_2025/7y7k_33668.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y7k_33668/03_2025/7y7k_33668.map" model { file = "/net/cci-nas-00/data/ceres_data/7y7k_33668/03_2025/7y7k_33668.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y7k_33668/03_2025/7y7k_33668.cif" } resolution = 4.4 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= -0.003 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 11 5.16 5 C 1832 2.51 5 N 505 2.21 5 O 594 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 2942 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1230 Classifications: {'peptide': 179} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 9, 'TRANS': 169} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 210 Unresolved non-hydrogen angles: 268 Unresolved non-hydrogen dihedrals: 186 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 7, 'ASN:plan1': 4, 'ASP:plan': 6, 'PHE:plan': 6, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 157 Chain: "B" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 953 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 6, 'TRANS': 125} Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 63 Chain: "C" Number of atoms: 759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 759 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 7, 'TRANS': 103} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 41 Time building chain proxies: 3.68, per 1000 atoms: 1.25 Number of scatterers: 2942 At special positions: 0 Unit cell: (56.58, 64.78, 104.14, 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 11 16.00 O 594 8.00 N 505 7.00 C 1832 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.01 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 97 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 90 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.74 Conformation dependent library (CDL) restraints added in 388.6 milliseconds 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 762 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 6 sheets defined 11.8% alpha, 30.3% 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 337 through 343 Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.118A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.651A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'B' and resid 65 through 67 No H-bonds generated for 'chain 'B' and resid 65 through 67' Processing helix chain 'B' and resid 88 through 92 Processing helix chain 'C' and resid 81 through 85 Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA2, first strand: chain 'B' and resid 3 through 7 removed outlier: 3.693A pdb=" N PHE B 80 " --> pdb=" O CYS B 22 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 11 through 12 removed outlier: 6.127A pdb=" N TRP B 36 " --> pdb=" O SER B 52 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N SER B 52 " --> pdb=" O TRP B 36 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N TRP B 38 " --> pdb=" O ILE B 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 17 through 23 Processing sheet with id=AA5, first strand: chain 'C' and resid 47 through 50 removed outlier: 6.235A pdb=" N TRP C 37 " --> pdb=" O LEU C 49 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N ASP C 34 " --> pdb=" O TYR C 93 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N TYR C 93 " --> pdb=" O ASP C 34 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 47 through 50 removed outlier: 6.235A pdb=" N TRP C 37 " --> pdb=" O LEU C 49 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N ASP C 34 " --> pdb=" O TYR C 93 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N TYR C 93 " --> pdb=" O ASP C 34 " (cutoff:3.500A) 114 hydrogen bonds defined for protein. 264 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: 0.74 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: 1.15 - 1.28: 494 1.28 - 1.42: 781 1.42 - 1.55: 1715 1.55 - 1.68: 3 1.68 - 1.81: 11 Bond restraints: 3004 Sorted by residual: bond pdb=" C ASN A 439 " pdb=" O ASN A 439 " ideal model delta sigma weight residual 1.236 1.151 0.085 1.18e-02 7.18e+03 5.20e+01 bond pdb=" C ARG B 102 " pdb=" N SER B 103 " ideal model delta sigma weight residual 1.332 1.288 0.045 1.40e-02 5.10e+03 1.01e+01 bond pdb=" C ASN A 439 " pdb=" N ASN A 440 " ideal model delta sigma weight residual 1.334 1.291 0.044 1.38e-02 5.25e+03 1.01e+01 bond pdb=" C LYS A 424 " pdb=" N LEU A 425 " ideal model delta sigma weight residual 1.335 1.265 0.070 3.04e-02 1.08e+03 5.32e+00 bond pdb=" CA GLU B 1 " pdb=" C GLU B 1 " ideal model delta sigma weight residual 1.525 1.481 0.044 2.10e-02 2.27e+03 4.49e+00 ... (remaining 2999 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 3702 2.41 - 4.81: 306 4.81 - 7.22: 78 7.22 - 9.62: 21 9.62 - 12.03: 5 Bond angle restraints: 4112 Sorted by residual: angle pdb=" N TYR A 489 " pdb=" CA TYR A 489 " pdb=" C TYR A 489 " ideal model delta sigma weight residual 109.65 119.96 -10.31 1.56e+00 4.11e-01 4.37e+01 angle pdb=" N THR A 478 " pdb=" CA THR A 478 " pdb=" C THR A 478 " ideal model delta sigma weight residual 109.06 119.62 -10.56 1.78e+00 3.16e-01 3.52e+01 angle pdb=" N TYR B 105 " pdb=" CA TYR B 105 " pdb=" C TYR B 105 " ideal model delta sigma weight residual 110.80 98.77 12.03 2.13e+00 2.20e-01 3.19e+01 angle pdb=" O ARG B 102 " pdb=" C ARG B 102 " pdb=" N SER B 103 " ideal model delta sigma weight residual 122.59 115.43 7.16 1.33e+00 5.65e-01 2.89e+01 angle pdb=" N PHE A 464 " pdb=" CA PHE A 464 " pdb=" C PHE A 464 " ideal model delta sigma weight residual 110.80 121.21 -10.41 2.13e+00 2.20e-01 2.39e+01 ... (remaining 4107 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.46: 1649 17.46 - 34.93: 87 34.93 - 52.39: 20 52.39 - 69.86: 9 69.86 - 87.32: 4 Dihedral angle restraints: 1769 sinusoidal: 564 harmonic: 1205 Sorted by residual: dihedral pdb=" CA GLN C 1 " pdb=" C GLN C 1 " pdb=" N SER C 2 " pdb=" CA SER C 2 " ideal model delta harmonic sigma weight residual -180.00 -161.81 -18.19 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA ALA C 86 " pdb=" C ALA C 86 " pdb=" N ASP C 87 " pdb=" CA ASP C 87 " ideal model delta harmonic sigma weight residual 180.00 162.64 17.36 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA ASN C 53 " pdb=" C ASN C 53 " pdb=" N ASN C 54 " pdb=" CA ASN C 54 " ideal model delta harmonic sigma weight residual 180.00 -162.92 -17.08 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 1766 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 285 0.056 - 0.112: 129 0.112 - 0.167: 42 0.167 - 0.223: 9 0.223 - 0.279: 7 Chirality restraints: 472 Sorted by residual: chirality pdb=" CA TYR A 489 " pdb=" N TYR A 489 " pdb=" C TYR A 489 " pdb=" CB TYR A 489 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" CA PRO A 479 " pdb=" N PRO A 479 " pdb=" C PRO A 479 " pdb=" CB PRO A 479 " both_signs ideal model delta sigma weight residual False 2.72 2.44 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CB VAL A 362 " pdb=" CA VAL A 362 " pdb=" CG1 VAL A 362 " pdb=" CG2 VAL A 362 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.78e+00 ... (remaining 469 not shown) Planarity restraints: 540 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 439 " -0.023 2.00e-02 2.50e+03 4.68e-02 2.19e+01 pdb=" C ASN A 439 " 0.081 2.00e-02 2.50e+03 pdb=" O ASN A 439 " -0.031 2.00e-02 2.50e+03 pdb=" N ASN A 440 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 490 " -0.077 5.00e-02 4.00e+02 1.16e-01 2.14e+01 pdb=" N PRO A 491 " 0.200 5.00e-02 4.00e+02 pdb=" CA PRO A 491 " -0.057 5.00e-02 4.00e+02 pdb=" CD PRO A 491 " -0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 38 " 0.024 2.00e-02 2.50e+03 2.81e-02 1.58e+01 pdb=" CG TYR C 38 " -0.069 2.00e-02 2.50e+03 pdb=" CD1 TYR C 38 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR C 38 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR C 38 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR C 38 " 0.011 2.00e-02 2.50e+03 pdb=" CZ TYR C 38 " 0.010 2.00e-02 2.50e+03 pdb=" OH TYR C 38 " -0.014 2.00e-02 2.50e+03 ... (remaining 537 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 568 2.75 - 3.29: 2907 3.29 - 3.83: 4888 3.83 - 4.36: 5365 4.36 - 4.90: 9159 Nonbonded interactions: 22887 Sorted by model distance: nonbonded pdb=" OG SER C 27 " pdb=" N THR C 96 " model vdw 2.215 3.120 nonbonded pdb=" O THR C 5 " pdb=" N THR C 23 " model vdw 2.251 3.120 nonbonded pdb=" O THR A 345 " pdb=" NH2 ARG A 509 " model vdw 2.253 3.120 nonbonded pdb=" NE2 GLN B 41 " pdb=" O LYS B 45 " model vdw 2.266 3.120 nonbonded pdb=" O CYS C 90 " pdb=" N GLY C 103 " model vdw 2.269 3.120 ... (remaining 22882 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: 4.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.480 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: 0.010 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: 21.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6429 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 : 0.010 0.104 3004 Z= 0.662 Angle : 1.632 12.028 4112 Z= 0.938 Chirality : 0.074 0.279 472 Planarity : 0.010 0.116 540 Dihedral : 13.106 87.323 992 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 33.93 Ramachandran Plot: Outliers : 3.61 % Allowed : 10.34 % Favored : 86.06 % Rotamer: Outliers : 3.90 % Allowed : 7.09 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.50 (0.38), residues: 416 helix: -3.92 (0.53), residues: 36 sheet: 0.24 (0.48), residues: 126 loop : -2.47 (0.34), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP B 49 HIS 0.007 0.002 HIS C 33 PHE 0.024 0.003 PHE A 456 TYR 0.069 0.006 TYR C 38 ARG 0.027 0.003 ARG C 63 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 95 TYR cc_start: 0.7862 (m-80) cc_final: 0.7483 (m-80) REVERT: C 16 GLN cc_start: 0.6542 (OUTLIER) cc_final: 0.5606 (pp30) REVERT: C 41 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8184 (tt) outliers start: 11 outliers final: 2 residues processed: 71 average time/residue: 0.2245 time to fit residues: 18.1229 Evaluate side-chains 29 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 25 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 0.2980 chunk 31 optimal weight: 6.9990 chunk 17 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 16 optimal weight: 0.4980 chunk 32 optimal weight: 6.9990 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 6.9990 chunk 23 optimal weight: 0.9980 chunk 37 optimal weight: 6.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 GLN C 33 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.062774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.054380 restraints weight = 27441.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.055651 restraints weight = 19296.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.056613 restraints weight = 14424.591| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6758 moved from start: 0.3923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3004 Z= 0.230 Angle : 0.794 7.863 4112 Z= 0.418 Chirality : 0.050 0.227 472 Planarity : 0.005 0.034 540 Dihedral : 5.565 19.446 454 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.96 % Allowed : 7.45 % Favored : 91.59 % Rotamer: Outliers : 0.71 % Allowed : 2.48 % Favored : 96.81 % 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: -1.87 (0.39), residues: 416 helix: -4.56 (0.37), residues: 24 sheet: 0.09 (0.45), residues: 135 loop : -1.73 (0.36), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 353 HIS 0.002 0.001 HIS B 100 PHE 0.011 0.002 PHE A 456 TYR 0.029 0.002 TYR C 38 ARG 0.004 0.001 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 39 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 95 TYR cc_start: 0.8610 (m-80) cc_final: 0.7874 (m-80) REVERT: B 107 TYR cc_start: 0.6300 (p90) cc_final: 0.5989 (p90) outliers start: 2 outliers final: 0 residues processed: 41 average time/residue: 0.2964 time to fit residues: 13.6604 Evaluate side-chains 23 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 37 optimal weight: 10.0000 chunk 0 optimal weight: 6.9990 chunk 30 optimal weight: 8.9990 chunk 4 optimal weight: 0.2980 chunk 6 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 chunk 22 optimal weight: 8.9990 chunk 19 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 overall best weight: 3.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 3 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 = 0.3568 r_free = 0.3568 target = 0.058929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.050679 restraints weight = 27427.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.051906 restraints weight = 19168.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.052803 restraints weight = 14197.666| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6919 moved from start: 0.5065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 3004 Z= 0.415 Angle : 0.904 7.503 4112 Z= 0.479 Chirality : 0.051 0.302 472 Planarity : 0.006 0.040 540 Dihedral : 6.445 20.362 454 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 21.30 Ramachandran Plot: Outliers : 0.96 % Allowed : 9.13 % Favored : 89.90 % Rotamer: Outliers : 0.35 % Allowed : 2.48 % Favored : 97.16 % 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: -1.94 (0.39), residues: 416 helix: -3.10 (0.63), residues: 37 sheet: -0.03 (0.44), residues: 126 loop : -1.74 (0.38), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 49 HIS 0.003 0.001 HIS B 100 PHE 0.014 0.002 PHE A 374 TYR 0.026 0.003 TYR C 38 ARG 0.008 0.001 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 28 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 6 GLU cc_start: 0.6597 (tt0) cc_final: 0.6058 (tt0) REVERT: B 107 TYR cc_start: 0.6351 (p90) cc_final: 0.6019 (p90) REVERT: C 40 GLN cc_start: 0.8714 (pt0) cc_final: 0.8072 (pm20) outliers start: 1 outliers final: 0 residues processed: 28 average time/residue: 0.2183 time to fit residues: 7.3042 Evaluate side-chains 17 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 0 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 3 optimal weight: 0.3980 chunk 30 optimal weight: 5.9990 chunk 14 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 34 optimal weight: 0.0570 chunk 12 optimal weight: 2.9990 chunk 36 optimal weight: 8.9990 chunk 2 optimal weight: 0.5980 overall best weight: 0.7900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 33 HIS ** 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 = 0.3639 r_free = 0.3639 target = 0.061057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.052318 restraints weight = 26909.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.053700 restraints weight = 18573.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.054659 restraints weight = 13623.951| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6811 moved from start: 0.5406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3004 Z= 0.172 Angle : 0.670 9.296 4112 Z= 0.347 Chirality : 0.048 0.351 472 Planarity : 0.004 0.045 540 Dihedral : 5.049 19.721 454 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.72 % Allowed : 6.49 % Favored : 92.79 % Rotamer: Outliers : 0.35 % Allowed : 2.13 % Favored : 97.52 % 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: -1.43 (0.41), residues: 416 helix: -2.38 (0.84), residues: 25 sheet: 0.08 (0.44), residues: 132 loop : -1.41 (0.40), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 353 HIS 0.004 0.002 HIS B 100 PHE 0.005 0.001 PHE A 486 TYR 0.016 0.001 TYR C 38 ARG 0.006 0.001 ARG C 95 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 29 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 20 LEU cc_start: 0.8385 (pp) cc_final: 0.7859 (mm) REVERT: B 95 TYR cc_start: 0.8673 (m-80) cc_final: 0.8040 (m-80) REVERT: B 107 TYR cc_start: 0.6373 (p90) cc_final: 0.6096 (p90) REVERT: C 40 GLN cc_start: 0.8765 (pt0) cc_final: 0.8036 (pm20) outliers start: 1 outliers final: 0 residues processed: 29 average time/residue: 0.1592 time to fit residues: 5.7493 Evaluate side-chains 20 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 7.9990 chunk 25 optimal weight: 30.0000 chunk 7 optimal weight: 1.9990 chunk 9 optimal weight: 0.0980 chunk 38 optimal weight: 8.9990 chunk 21 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 37 optimal weight: 9.9990 chunk 5 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 33 HIS ** 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 = 0.3601 r_free = 0.3601 target = 0.059870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.051445 restraints weight = 26815.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.052837 restraints weight = 18310.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.053793 restraints weight = 13357.861| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6848 moved from start: 0.5702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3004 Z= 0.203 Angle : 0.665 8.460 4112 Z= 0.344 Chirality : 0.047 0.308 472 Planarity : 0.004 0.046 540 Dihedral : 5.033 18.910 454 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.72 % Allowed : 7.45 % Favored : 91.83 % Rotamer: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % 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: -1.46 (0.42), residues: 416 helix: -2.38 (0.81), residues: 31 sheet: 0.16 (0.45), residues: 138 loop : -1.50 (0.41), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 353 HIS 0.002 0.001 HIS C 33 PHE 0.007 0.001 PHE A 338 TYR 0.035 0.002 TYR C 100 ARG 0.005 0.001 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 20 LEU cc_start: 0.8586 (pp) cc_final: 0.7893 (mm) REVERT: B 107 TYR cc_start: 0.6341 (p90) cc_final: 0.6065 (p90) REVERT: C 40 GLN cc_start: 0.8843 (pt0) cc_final: 0.8129 (pm20) outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.1277 time to fit residues: 4.5432 Evaluate side-chains 20 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 4 optimal weight: 10.0000 chunk 12 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 22 optimal weight: 0.0030 chunk 31 optimal weight: 0.0050 chunk 3 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 34 optimal weight: 10.0000 overall best weight: 0.5206 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 ASN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.061302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.052620 restraints weight = 26882.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.054034 restraints weight = 18436.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.055017 restraints weight = 13477.636| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6808 moved from start: 0.6040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3004 Z= 0.133 Angle : 0.608 8.155 4112 Z= 0.306 Chirality : 0.047 0.325 472 Planarity : 0.004 0.047 540 Dihedral : 4.340 18.863 454 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.72 % Allowed : 5.05 % Favored : 94.23 % Rotamer: Outliers : 0.35 % Allowed : 0.71 % Favored : 98.94 % 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: -1.41 (0.41), residues: 416 helix: -2.08 (0.97), residues: 25 sheet: 0.50 (0.46), residues: 129 loop : -1.67 (0.39), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 436 HIS 0.001 0.001 HIS B 100 PHE 0.005 0.001 PHE A 490 TYR 0.015 0.001 TYR C 100 ARG 0.003 0.001 ARG C 95 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 34 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 487 ASN cc_start: 0.5607 (OUTLIER) cc_final: 0.5045 (m110) REVERT: B 95 TYR cc_start: 0.8815 (m-80) cc_final: 0.8006 (m-10) REVERT: B 107 TYR cc_start: 0.6314 (p90) cc_final: 0.6025 (p90) REVERT: C 17 ARG cc_start: 0.9203 (ttt-90) cc_final: 0.8978 (tpt-90) REVERT: C 40 GLN cc_start: 0.8776 (pt0) cc_final: 0.8235 (pm20) outliers start: 1 outliers final: 0 residues processed: 35 average time/residue: 0.2306 time to fit residues: 9.4263 Evaluate side-chains 23 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 22 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 1 optimal weight: 0.0010 chunk 7 optimal weight: 3.9990 chunk 32 optimal weight: 9.9990 chunk 29 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 chunk 13 optimal weight: 7.9990 chunk 20 optimal weight: 9.9990 chunk 38 optimal weight: 5.9990 chunk 34 optimal weight: 0.0570 overall best weight: 1.8108 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 ASN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.058971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.050724 restraints weight = 27848.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.052031 restraints weight = 19145.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.053004 restraints weight = 13944.688| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6865 moved from start: 0.6331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 3004 Z= 0.238 Angle : 0.663 7.459 4112 Z= 0.340 Chirality : 0.046 0.179 472 Planarity : 0.004 0.046 540 Dihedral : 4.942 19.098 454 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.72 % Allowed : 8.17 % Favored : 91.11 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % 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: -1.56 (0.41), residues: 416 helix: -2.27 (0.83), residues: 31 sheet: 0.44 (0.46), residues: 129 loop : -1.76 (0.40), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 49 HIS 0.001 0.001 HIS B 100 PHE 0.024 0.002 PHE A 486 TYR 0.021 0.002 TYR C 100 ARG 0.006 0.001 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 20 LEU cc_start: 0.8523 (pp) cc_final: 0.7848 (mm) REVERT: B 95 TYR cc_start: 0.8763 (m-80) cc_final: 0.8135 (m-80) REVERT: B 107 TYR cc_start: 0.6379 (p90) cc_final: 0.6074 (p90) REVERT: C 40 GLN cc_start: 0.8819 (pt0) cc_final: 0.8180 (pm20) outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.2069 time to fit residues: 6.4148 Evaluate side-chains 18 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 4 optimal weight: 0.7980 chunk 6 optimal weight: 0.0050 chunk 23 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 31 optimal weight: 0.0170 chunk 14 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 38 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 overall best weight: 0.4232 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** 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 = 0.3650 r_free = 0.3650 target = 0.060607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.051970 restraints weight = 26940.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.053380 restraints weight = 18674.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.054398 restraints weight = 13731.355| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6803 moved from start: 0.6596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3004 Z= 0.134 Angle : 0.600 7.322 4112 Z= 0.299 Chirality : 0.046 0.253 472 Planarity : 0.004 0.048 540 Dihedral : 4.242 18.138 454 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.48 % Allowed : 6.01 % Favored : 93.51 % Rotamer: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % 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: -1.34 (0.42), residues: 416 helix: -1.41 (1.19), residues: 19 sheet: 0.67 (0.46), residues: 131 loop : -1.79 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 436 HIS 0.000 0.000 HIS C 33 PHE 0.019 0.001 PHE A 486 TYR 0.019 0.001 TYR C 100 ARG 0.002 0.000 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 95 TYR cc_start: 0.8826 (m-80) cc_final: 0.8000 (m-10) REVERT: B 107 TYR cc_start: 0.6353 (p90) cc_final: 0.6043 (p90) REVERT: B 120 ASP cc_start: 0.8270 (p0) cc_final: 0.7677 (m-30) REVERT: C 40 GLN cc_start: 0.8821 (pt0) cc_final: 0.8291 (pm20) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.2169 time to fit residues: 7.4958 Evaluate side-chains 25 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 10.0000 chunk 23 optimal weight: 0.6980 chunk 13 optimal weight: 0.0060 chunk 35 optimal weight: 6.9990 chunk 21 optimal weight: 0.9980 chunk 25 optimal weight: 7.9990 chunk 6 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 29 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** 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 = 0.3643 r_free = 0.3643 target = 0.060452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.051935 restraints weight = 26824.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.053283 restraints weight = 18575.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.054283 restraints weight = 13706.117| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6819 moved from start: 0.6689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3004 Z= 0.142 Angle : 0.594 7.503 4112 Z= 0.296 Chirality : 0.046 0.251 472 Planarity : 0.004 0.047 540 Dihedral : 4.139 17.204 454 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.48 % Allowed : 6.73 % Favored : 92.79 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % 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: -1.31 (0.41), residues: 416 helix: -1.95 (0.96), residues: 25 sheet: 0.72 (0.46), residues: 129 loop : -1.70 (0.39), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 436 HIS 0.001 0.000 HIS B 100 PHE 0.017 0.001 PHE A 486 TYR 0.015 0.001 TYR C 100 ARG 0.003 0.001 ARG C 17 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 95 TYR cc_start: 0.8838 (m-80) cc_final: 0.7990 (m-10) REVERT: B 107 TYR cc_start: 0.6417 (p90) cc_final: 0.6086 (p90) REVERT: C 40 GLN cc_start: 0.8805 (pt0) cc_final: 0.8263 (pm20) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.2326 time to fit residues: 7.7628 Evaluate side-chains 24 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 15 optimal weight: 0.0170 chunk 12 optimal weight: 7.9990 chunk 4 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 37 optimal weight: 9.9990 chunk 21 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 3 optimal weight: 0.1980 overall best weight: 0.5420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** 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 = 0.3648 r_free = 0.3648 target = 0.060614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.052249 restraints weight = 26984.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.053561 restraints weight = 18826.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.054539 restraints weight = 14045.521| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6808 moved from start: 0.6882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 3004 Z= 0.130 Angle : 0.579 7.580 4112 Z= 0.288 Chirality : 0.046 0.237 472 Planarity : 0.004 0.047 540 Dihedral : 3.972 17.613 454 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.48 % Allowed : 6.01 % Favored : 93.51 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.22 (0.41), residues: 416 helix: -1.56 (1.04), residues: 25 sheet: 0.78 (0.46), residues: 131 loop : -1.69 (0.38), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 HIS 0.001 0.000 HIS B 100 PHE 0.017 0.001 PHE A 486 TYR 0.016 0.001 TYR C 100 ARG 0.002 0.000 ARG C 17 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 20 LEU cc_start: 0.8738 (pp) cc_final: 0.8029 (mt) REVERT: B 107 TYR cc_start: 0.6454 (p90) cc_final: 0.6087 (p90) REVERT: C 40 GLN cc_start: 0.8786 (pt0) cc_final: 0.8249 (pm20) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.2104 time to fit residues: 7.2693 Evaluate side-chains 23 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 0.0010 chunk 27 optimal weight: 3.9990 chunk 21 optimal weight: 0.0980 chunk 24 optimal weight: 7.9990 chunk 29 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 overall best weight: 1.0190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** 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 = 0.3627 r_free = 0.3627 target = 0.059968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.051628 restraints weight = 26293.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.052935 restraints weight = 18234.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.053924 restraints weight = 13475.883| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6815 moved from start: 0.6998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 3004 Z= 0.164 Angle : 0.592 7.501 4112 Z= 0.297 Chirality : 0.045 0.240 472 Planarity : 0.004 0.047 540 Dihedral : 4.168 17.867 454 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.93 % Favored : 91.83 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.33 (0.42), residues: 416 helix: -2.01 (0.87), residues: 31 sheet: 0.35 (0.46), residues: 138 loop : -1.53 (0.40), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 436 HIS 0.002 0.001 HIS B 100 PHE 0.016 0.001 PHE A 486 TYR 0.014 0.001 TYR C 100 ARG 0.004 0.001 ARG C 17 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1532.14 seconds wall clock time: 27 minutes 19.19 seconds (1639.19 seconds total)