Sun 23 Dec 22:23:10 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vkh-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vkh-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vkh-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkh-3.2-parrot-hancs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkh-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkh-3.2-parrot-hancs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Sun 23 Dec 22:23:19 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkh-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkh-3.2-parrot-hancs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 395 and 0 Target number of residues in the AU: 395 Target solvent content: 0.5757 Checking the provided sequence file Detected sequence length: 273 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 546 Adjusted target solvent content: 0.41 Input MTZ file: 1vkh-3.2-parrot-hancs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 4 Cell parameters: 41.965 85.956 70.476 90.000 97.713 90.000 Input sequence file: 1vkh-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 4368 target number of atoms Had to go as low as 0.60 sigma, to complete atoms search. ARP/wARP will be iterated with REFMAC5 50 refinement / model update cycles will be run in total. Atoms will be removed below 1.0 sigma in 2mFoDFc map and added above 3.2 sigma in mFoDFc map. Refmac Refinement Parameters 3 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Conditional restraints will be used Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling with no bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Side chain docking will be performed from autobuilding cycle number 1 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 19.289 3.200 Wilson plot Bfac: 43.34 8219 reflections ( 99.49 % complete ) and 0 restraints for refining 4848 atoms. Observations/parameters ratio is 0.42 ------------------------------------------------------ Starting model: R = 0.3195 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2742 (Rfree = 0.000) for 4848 atoms. Found 43 (43 requested) and removed 107 (21 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.84 3.21 Search for helices and strands: 0 residues in 0 chains, 4917 seeds are put forward NCS extension: 0 residues added, 4917 seeds are put forward Round 1: 231 peptides, 44 chains. Longest chain 10 peptides. Score 0.360 Round 2: 300 peptides, 48 chains. Longest chain 16 peptides. Score 0.514 Round 3: 316 peptides, 48 chains. Longest chain 18 peptides. Score 0.555 Round 4: 331 peptides, 47 chains. Longest chain 15 peptides. Score 0.601 Round 5: 336 peptides, 41 chains. Longest chain 28 peptides. Score 0.669 Taking the results from Round 5 Chains 43, Residues 295, Estimated correctness of the model 58.3 % 3 chains (56 residues) have been docked in sequence ------------------------------------------------------ 8219 reflections ( 99.49 % complete ) and 7984 restraints for refining 3986 atoms. 6578 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2511 (Rfree = 0.000) for 3986 atoms. Found 29 (35 requested) and removed 32 (17 requested) atoms. Cycle 2: After refmac, R = 0.2287 (Rfree = 0.000) for 3946 atoms. Found 9 (35 requested) and removed 20 (17 requested) atoms. Cycle 3: After refmac, R = 0.2222 (Rfree = 0.000) for 3919 atoms. Found 12 (35 requested) and removed 21 (17 requested) atoms. Cycle 4: After refmac, R = 0.2179 (Rfree = 0.000) for 3903 atoms. Found 13 (35 requested) and removed 18 (17 requested) atoms. Cycle 5: After refmac, R = 0.2123 (Rfree = 0.000) for 3892 atoms. Found 12 (34 requested) and removed 19 (17 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.85 3.22 Search for helices and strands: 0 residues in 0 chains, 4050 seeds are put forward NCS extension: 16 residues added (11 deleted due to clashes), 4066 seeds are put forward Round 1: 304 peptides, 46 chains. Longest chain 16 peptides. Score 0.547 Round 2: 334 peptides, 44 chains. Longest chain 24 peptides. Score 0.637 Round 3: 341 peptides, 44 chains. Longest chain 23 peptides. Score 0.652 Round 4: 340 peptides, 45 chains. Longest chain 24 peptides. Score 0.640 Round 5: 323 peptides, 43 chains. Longest chain 25 peptides. Score 0.623 Taking the results from Round 3 Chains 45, Residues 297, Estimated correctness of the model 54.3 % 3 chains (46 residues) have been docked in sequence ------------------------------------------------------ 8219 reflections ( 99.49 % complete ) and 8282 restraints for refining 3985 atoms. 6921 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2363 (Rfree = 0.000) for 3985 atoms. Found 26 (35 requested) and removed 26 (17 requested) atoms. Cycle 7: After refmac, R = 0.2245 (Rfree = 0.000) for 3975 atoms. Found 15 (35 requested) and removed 22 (17 requested) atoms. Cycle 8: After refmac, R = 0.2178 (Rfree = 0.000) for 3964 atoms. Found 15 (35 requested) and removed 17 (17 requested) atoms. Cycle 9: After refmac, R = 0.2129 (Rfree = 0.000) for 3959 atoms. Found 12 (35 requested) and removed 18 (17 requested) atoms. Cycle 10: After refmac, R = 0.2086 (Rfree = 0.000) for 3949 atoms. Found 9 (35 requested) and removed 18 (17 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.90 3.27 Search for helices and strands: 0 residues in 0 chains, 4081 seeds are put forward NCS extension: 23 residues added (3 deleted due to clashes), 4104 seeds are put forward Round 1: 285 peptides, 37 chains. Longest chain 20 peptides. Score 0.597 Round 2: 311 peptides, 34 chains. Longest chain 27 peptides. Score 0.682 Round 3: 326 peptides, 39 chains. Longest chain 23 peptides. Score 0.667 Round 4: 329 peptides, 36 chains. Longest chain 38 peptides. Score 0.699 Round 5: 333 peptides, 40 chains. Longest chain 23 peptides. Score 0.672 Taking the results from Round 4 Chains 38, Residues 293, Estimated correctness of the model 65.0 % 3 chains (53 residues) have been docked in sequence ------------------------------------------------------ 8219 reflections ( 99.49 % complete ) and 8269 restraints for refining 3987 atoms. 6895 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2354 (Rfree = 0.000) for 3987 atoms. Found 21 (35 requested) and removed 25 (17 requested) atoms. Cycle 12: After refmac, R = 0.2158 (Rfree = 0.000) for 3974 atoms. Found 17 (35 requested) and removed 20 (17 requested) atoms. Cycle 13: After refmac, R = 0.2158 (Rfree = 0.000) for 3962 atoms. Found 16 (35 requested) and removed 20 (17 requested) atoms. Cycle 14: After refmac, R = 0.2101 (Rfree = 0.000) for 3956 atoms. Found 12 (35 requested) and removed 17 (17 requested) atoms. Cycle 15: After refmac, R = 0.2064 (Rfree = 0.000) for 3947 atoms. Found 6 (35 requested) and removed 19 (17 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.87 3.24 Search for helices and strands: 0 residues in 0 chains, 4059 seeds are put forward NCS extension: 21 residues added (10 deleted due to clashes), 4080 seeds are put forward Round 1: 303 peptides, 45 chains. Longest chain 20 peptides. Score 0.555 Round 2: 322 peptides, 42 chains. Longest chain 22 peptides. Score 0.631 Round 3: 345 peptides, 45 chains. Longest chain 24 peptides. Score 0.651 Round 4: 327 peptides, 42 chains. Longest chain 20 peptides. Score 0.641 Round 5: 325 peptides, 37 chains. Longest chain 28 peptides. Score 0.683 Taking the results from Round 5 Chains 38, Residues 288, Estimated correctness of the model 61.5 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 8219 reflections ( 99.49 % complete ) and 8827 restraints for refining 3987 atoms. 7652 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2239 (Rfree = 0.000) for 3987 atoms. Found 30 (35 requested) and removed 21 (17 requested) atoms. Cycle 17: After refmac, R = 0.2062 (Rfree = 0.000) for 3986 atoms. Found 13 (35 requested) and removed 19 (17 requested) atoms. Cycle 18: After refmac, R = 0.2030 (Rfree = 0.000) for 3974 atoms. Found 11 (35 requested) and removed 17 (17 requested) atoms. Cycle 19: After refmac, R = 0.1977 (Rfree = 0.000) for 3966 atoms. Found 8 (35 requested) and removed 19 (17 requested) atoms. Cycle 20: After refmac, R = 0.1967 (Rfree = 0.000) for 3952 atoms. Found 16 (35 requested) and removed 17 (17 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.90 3.27 Search for helices and strands: 0 residues in 0 chains, 4113 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 4131 seeds are put forward Round 1: 291 peptides, 41 chains. Longest chain 22 peptides. Score 0.569 Round 2: 311 peptides, 40 chains. Longest chain 17 peptides. Score 0.626 Round 3: 310 peptides, 37 chains. Longest chain 25 peptides. Score 0.653 Round 4: 309 peptides, 40 chains. Longest chain 22 peptides. Score 0.622 Round 5: 306 peptides, 38 chains. Longest chain 21 peptides. Score 0.635 Taking the results from Round 3 Chains 37, Residues 273, Estimated correctness of the model 54.6 % 2 chains (35 residues) have been docked in sequence ------------------------------------------------------ 8219 reflections ( 99.49 % complete ) and 8657 restraints for refining 3987 atoms. 7445 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2210 (Rfree = 0.000) for 3987 atoms. Found 33 (35 requested) and removed 23 (17 requested) atoms. Cycle 22: After refmac, R = 0.2004 (Rfree = 0.000) for 3992 atoms. Found 8 (35 requested) and removed 17 (17 requested) atoms. Cycle 23: After refmac, R = 0.1947 (Rfree = 0.000) for 3978 atoms. Found 11 (35 requested) and removed 17 (17 requested) atoms. Cycle 24: After refmac, R = 0.1915 (Rfree = 0.000) for 3967 atoms. Found 7 (35 requested) and removed 17 (17 requested) atoms. Cycle 25: After refmac, R = 0.1907 (Rfree = 0.000) for 3953 atoms. Found 9 (35 requested) and removed 17 (17 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.89 3.26 Search for helices and strands: 0 residues in 0 chains, 4077 seeds are put forward NCS extension: 21 residues added (3 deleted due to clashes), 4098 seeds are put forward Round 1: 260 peptides, 40 chains. Longest chain 16 peptides. Score 0.499 Round 2: 288 peptides, 36 chains. Longest chain 18 peptides. Score 0.615 Round 3: 281 peptides, 38 chains. Longest chain 19 peptides. Score 0.577 Round 4: 302 peptides, 35 chains. Longest chain 20 peptides. Score 0.655 Round 5: 312 peptides, 38 chains. Longest chain 24 peptides. Score 0.647 Taking the results from Round 4 Chains 36, Residues 267, Estimated correctness of the model 55.0 % 2 chains (31 residues) have been docked in sequence ------------------------------------------------------ 8219 reflections ( 99.49 % complete ) and 8575 restraints for refining 3987 atoms. 7404 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2155 (Rfree = 0.000) for 3987 atoms. Found 30 (35 requested) and removed 20 (17 requested) atoms. Cycle 27: After refmac, R = 0.2009 (Rfree = 0.000) for 3992 atoms. Found 9 (35 requested) and removed 18 (17 requested) atoms. Cycle 28: After refmac, R = 0.1956 (Rfree = 0.000) for 3979 atoms. Found 10 (35 requested) and removed 18 (17 requested) atoms. Cycle 29: After refmac, R = 0.1962 (Rfree = 0.000) for 3964 atoms. Found 7 (35 requested) and removed 18 (17 requested) atoms. Cycle 30: After refmac, R = 0.1927 (Rfree = 0.000) for 3953 atoms. Failed to save intermediate PDB Found 11 (35 requested) and removed 17 (17 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.89 3.26 Search for helices and strands: 0 residues in 0 chains, 4059 seeds are put forward NCS extension: 16 residues added (7 deleted due to clashes), 4075 seeds are put forward Round 1: 252 peptides, 41 chains. Longest chain 15 peptides. Score 0.464 Round 2: 284 peptides, 38 chains. Longest chain 24 peptides. Score 0.584 Round 3: 284 peptides, 39 chains. Longest chain 17 peptides. Score 0.573 Round 4: 272 peptides, 36 chains. Longest chain 20 peptides. Score 0.577 Round 5: 269 peptides, 36 chains. Longest chain 18 peptides. Score 0.569 Taking the results from Round 2 Chains 38, Residues 246, Estimated correctness of the model 36.7 % 1 chains (15 residues) have been docked in sequence ------------------------------------------------------ 8219 reflections ( 99.49 % complete ) and 8969 restraints for refining 3985 atoms. 7951 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1999 (Rfree = 0.000) for 3985 atoms. Found 27 (35 requested) and removed 20 (17 requested) atoms. Cycle 32: After refmac, R = 0.1906 (Rfree = 0.000) for 3987 atoms. Found 9 (35 requested) and removed 18 (17 requested) atoms. Cycle 33: After refmac, R = 0.1918 (Rfree = 0.000) for 3973 atoms. Found 19 (35 requested) and removed 17 (17 requested) atoms. Cycle 34: After refmac, R = 0.2193 (Rfree = 0.000) for 3971 atoms. Found 35 (35 requested) and removed 19 (17 requested) atoms. Cycle 35: After refmac, R = 0.2223 (Rfree = 0.000) for 3984 atoms. Found 35 (35 requested) and removed 17 (17 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.84 3.21 Search for helices and strands: 0 residues in 0 chains, 4131 seeds are put forward NCS extension: 25 residues added (4 deleted due to clashes), 4156 seeds are put forward Round 1: 247 peptides, 43 chains. Longest chain 17 peptides. Score 0.424 Round 2: 279 peptides, 42 chains. Longest chain 22 peptides. Score 0.527 Round 3: 283 peptides, 41 chains. Longest chain 18 peptides. Score 0.549 Round 4: 278 peptides, 41 chains. Longest chain 14 peptides. Score 0.536 Round 5: 263 peptides, 40 chains. Longest chain 14 peptides. Score 0.507 Taking the results from Round 3 Chains 41, Residues 242, Estimated correctness of the model 26.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8219 reflections ( 99.49 % complete ) and 9229 restraints for refining 3987 atoms. 8302 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2001 (Rfree = 0.000) for 3987 atoms. Found 26 (35 requested) and removed 17 (17 requested) atoms. Cycle 37: After refmac, R = 0.1856 (Rfree = 0.000) for 3993 atoms. Found 10 (35 requested) and removed 18 (17 requested) atoms. Cycle 38: After refmac, R = 0.1803 (Rfree = 0.000) for 3981 atoms. Found 7 (35 requested) and removed 22 (17 requested) atoms. Cycle 39: After refmac, R = 0.1765 (Rfree = 0.000) for 3964 atoms. Found 13 (35 requested) and removed 17 (17 requested) atoms. Cycle 40: After refmac, R = 0.1735 (Rfree = 0.000) for 3958 atoms. Found 5 (35 requested) and removed 18 (17 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.89 3.26 Search for helices and strands: 0 residues in 0 chains, 4043 seeds are put forward NCS extension: 16 residues added (3 deleted due to clashes), 4059 seeds are put forward Round 1: 217 peptides, 38 chains. Longest chain 18 peptides. Score 0.397 Round 2: 269 peptides, 42 chains. Longest chain 16 peptides. Score 0.500 Round 3: 267 peptides, 41 chains. Longest chain 20 peptides. Score 0.506 Round 4: 271 peptides, 42 chains. Longest chain 13 peptides. Score 0.505 Round 5: 279 peptides, 37 chains. Longest chain 23 peptides. Score 0.583 Taking the results from Round 5 Chains 38, Residues 242, Estimated correctness of the model 36.4 % 1 chains (17 residues) have been docked in sequence ------------------------------------------------------ 8219 reflections ( 99.49 % complete ) and 8906 restraints for refining 3987 atoms. 7898 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2058 (Rfree = 0.000) for 3987 atoms. Found 29 (35 requested) and removed 23 (17 requested) atoms. Cycle 42: After refmac, R = 0.1830 (Rfree = 0.000) for 3987 atoms. Found 16 (35 requested) and removed 19 (17 requested) atoms. Cycle 43: After refmac, R = 0.1826 (Rfree = 0.000) for 3980 atoms. Found 13 (35 requested) and removed 17 (17 requested) atoms. Cycle 44: After refmac, R = 0.1769 (Rfree = 0.000) for 3974 atoms. Found 10 (35 requested) and removed 18 (17 requested) atoms. Cycle 45: After refmac, R = 0.1743 (Rfree = 0.000) for 3965 atoms. Found 9 (35 requested) and removed 17 (17 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.90 3.27 Search for helices and strands: 0 residues in 0 chains, 4062 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 4078 seeds are put forward Round 1: 222 peptides, 37 chains. Longest chain 20 peptides. Score 0.426 Round 2: 228 peptides, 33 chains. Longest chain 12 peptides. Score 0.495 Round 3: 249 peptides, 35 chains. Longest chain 23 peptides. Score 0.529 Round 4: 235 peptides, 33 chains. Longest chain 23 peptides. Score 0.515 Round 5: 244 peptides, 35 chains. Longest chain 22 peptides. Score 0.515 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 36, Residues 214, Estimated correctness of the model 20.5 % 1 chains (17 residues) have been docked in sequence Sequence coverage is 7 % Consider running further cycles of model building using 1vkh-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 8219 reflections ( 99.49 % complete ) and 8972 restraints for refining 3958 atoms. 8074 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1924 (Rfree = 0.000) for 3958 atoms. Found 0 (35 requested) and removed 17 (17 requested) atoms. Cycle 47: After refmac, R = 0.1884 (Rfree = 0.000) for 3941 atoms. Found 0 (35 requested) and removed 7 (17 requested) atoms. Cycle 48: After refmac, R = 0.1897 (Rfree = 0.000) for 3933 atoms. Found 0 (35 requested) and removed 3 (17 requested) atoms. Cycle 49: After refmac, R = 0.1849 (Rfree = 0.000) for 3928 atoms. TimeTaking 60.67