null Sun 23 Dec 22:23:02 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 2fna-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2fna-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2fna-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fna-4.0-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/2fna-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fna-4.0-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 22:23:12 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/2fna-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fna-4.0-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 495 and 0 Target number of residues in the AU: 495 Target solvent content: 0.6787 Checking the provided sequence file Detected sequence length: 357 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 714 Adjusted target solvent content: 0.54 Input MTZ file: 2fna-4.0-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: 55.380 108.390 70.600 90.000 100.307 90.000 Input sequence file: 2fna-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 5712 target number of atoms Had to go as low as 0.80 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: 69.461 4.000 Wilson plot Bfac: 99.62 6907 reflections ( 98.46 % complete ) and 0 restraints for refining 6303 atoms. Observations/parameters ratio is 0.27 ------------------------------------------------------ Starting model: R = 0.3415 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3390 (Rfree = 0.000) for 6303 atoms. Found 29 (29 requested) and removed 61 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.91 3.71 Search for helices and strands: 0 residues in 0 chains, 6421 seeds are put forward NCS extension: 0 residues added, 6421 seeds are put forward Round 1: 227 peptides, 48 chains. Longest chain 9 peptides. Score 0.252 Round 2: 277 peptides, 47 chains. Longest chain 13 peptides. Score 0.370 Round 3: 286 peptides, 48 chains. Longest chain 15 peptides. Score 0.380 Round 4: 287 peptides, 44 chains. Longest chain 20 peptides. Score 0.417 Round 5: 301 peptides, 42 chains. Longest chain 18 peptides. Score 0.460 Taking the results from Round 5 Chains 42, Residues 259, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6907 reflections ( 98.46 % complete ) and 12540 restraints for refining 5154 atoms. 11546 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2904 (Rfree = 0.000) for 5154 atoms. Found 23 (24 requested) and removed 40 (12 requested) atoms. Cycle 2: After refmac, R = 0.2817 (Rfree = 0.000) for 5038 atoms. Found 24 (24 requested) and removed 39 (12 requested) atoms. Cycle 3: After refmac, R = 0.2319 (Rfree = 0.000) for 4957 atoms. Found 17 (23 requested) and removed 23 (11 requested) atoms. Cycle 4: After refmac, R = 0.2499 (Rfree = 0.000) for 4896 atoms. Found 23 (23 requested) and removed 25 (11 requested) atoms. Cycle 5: After refmac, R = 0.2354 (Rfree = 0.000) for 4841 atoms. Found 23 (23 requested) and removed 24 (11 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.86 3.66 Search for helices and strands: 0 residues in 0 chains, 5024 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 5044 seeds are put forward Round 1: 265 peptides, 52 chains. Longest chain 10 peptides. Score 0.300 Round 2: 330 peptides, 55 chains. Longest chain 13 peptides. Score 0.406 Round 3: 333 peptides, 49 chains. Longest chain 14 peptides. Score 0.461 Round 4: 333 peptides, 49 chains. Longest chain 16 peptides. Score 0.461 Round 5: 337 peptides, 49 chains. Longest chain 15 peptides. Score 0.469 Taking the results from Round 5 Chains 49, Residues 288, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6907 reflections ( 98.46 % complete ) and 11599 restraints for refining 5004 atoms. 10496 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2680 (Rfree = 0.000) for 5004 atoms. Found 23 (23 requested) and removed 57 (11 requested) atoms. Cycle 7: After refmac, R = 0.2447 (Rfree = 0.000) for 4906 atoms. Found 23 (23 requested) and removed 35 (11 requested) atoms. Cycle 8: After refmac, R = 0.2011 (Rfree = 0.000) for 4849 atoms. Found 17 (23 requested) and removed 21 (11 requested) atoms. Cycle 9: After refmac, R = 0.2416 (Rfree = 0.000) for 4816 atoms. Found 23 (23 requested) and removed 22 (11 requested) atoms. Cycle 10: After refmac, R = 0.1955 (Rfree = 0.000) for 4781 atoms. Found 21 (22 requested) and removed 15 (11 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.91 3.71 Search for helices and strands: 0 residues in 0 chains, 4960 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 4974 seeds are put forward Round 1: 270 peptides, 54 chains. Longest chain 12 peptides. Score 0.292 Round 2: 316 peptides, 56 chains. Longest chain 13 peptides. Score 0.370 Round 3: 313 peptides, 53 chains. Longest chain 14 peptides. Score 0.390 Round 4: 300 peptides, 47 chains. Longest chain 13 peptides. Score 0.416 Round 5: 331 peptides, 50 chains. Longest chain 14 peptides. Score 0.450 Taking the results from Round 5 Chains 50, Residues 281, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6907 reflections ( 98.46 % complete ) and 11141 restraints for refining 4940 atoms. 10067 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2588 (Rfree = 0.000) for 4940 atoms. Found 23 (23 requested) and removed 55 (11 requested) atoms. Cycle 12: After refmac, R = 0.2544 (Rfree = 0.000) for 4837 atoms. Found 23 (23 requested) and removed 25 (11 requested) atoms. Cycle 13: After refmac, R = 0.2345 (Rfree = 0.000) for 4775 atoms. Found 22 (22 requested) and removed 23 (11 requested) atoms. Cycle 14: After refmac, R = 0.2001 (Rfree = 0.000) for 4723 atoms. Found 13 (22 requested) and removed 15 (11 requested) atoms. Cycle 15: After refmac, R = 0.2260 (Rfree = 0.000) for 4695 atoms. Found 22 (22 requested) and removed 27 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.97 3.76 Search for helices and strands: 0 residues in 0 chains, 4832 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 4846 seeds are put forward Round 1: 248 peptides, 48 chains. Longest chain 12 peptides. Score 0.300 Round 2: 292 peptides, 52 chains. Longest chain 12 peptides. Score 0.357 Round 3: 300 peptides, 46 chains. Longest chain 17 peptides. Score 0.425 Round 4: 287 peptides, 40 chains. Longest chain 20 peptides. Score 0.451 Round 5: 280 peptides, 49 chains. Longest chain 12 peptides. Score 0.359 Taking the results from Round 4 Chains 40, Residues 247, Estimated correctness of the model 0.0 % 1 chains (19 residues) have been docked in sequence ------------------------------------------------------ 6907 reflections ( 98.46 % complete ) and 10906 restraints for refining 4833 atoms. 9877 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2673 (Rfree = 0.000) for 4833 atoms. Found 22 (22 requested) and removed 44 (11 requested) atoms. Cycle 17: After refmac, R = 0.2332 (Rfree = 0.000) for 4747 atoms. Found 22 (22 requested) and removed 24 (11 requested) atoms. Cycle 18: After refmac, R = 0.1851 (Rfree = 0.000) for 4695 atoms. Found 12 (22 requested) and removed 15 (11 requested) atoms. Cycle 19: After refmac, R = 0.2027 (Rfree = 0.000) for 4666 atoms. Found 18 (22 requested) and removed 17 (11 requested) atoms. Cycle 20: After refmac, R = 0.1976 (Rfree = 0.000) for 4646 atoms. Found 22 (22 requested) and removed 19 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.83 3.63 Search for helices and strands: 0 residues in 0 chains, 4817 seeds are put forward NCS extension: 23 residues added (2 deleted due to clashes), 4840 seeds are put forward Round 1: 258 peptides, 53 chains. Longest chain 10 peptides. Score 0.275 Round 2: 308 peptides, 56 chains. Longest chain 10 peptides. Score 0.354 Round 3: 323 peptides, 52 chains. Longest chain 15 peptides. Score 0.418 Round 4: 323 peptides, 49 chains. Longest chain 14 peptides. Score 0.443 Round 5: 309 peptides, 49 chains. Longest chain 14 peptides. Score 0.416 Taking the results from Round 4 Chains 49, Residues 274, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6907 reflections ( 98.46 % complete ) and 11380 restraints for refining 4981 atoms. 10333 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2389 (Rfree = 0.000) for 4981 atoms. Found 23 (23 requested) and removed 35 (11 requested) atoms. Cycle 22: After refmac, R = 0.2180 (Rfree = 0.000) for 4922 atoms. Found 23 (23 requested) and removed 20 (11 requested) atoms. Cycle 23: After refmac, R = 0.2254 (Rfree = 0.000) for 4894 atoms. Found 23 (23 requested) and removed 23 (11 requested) atoms. Cycle 24: After refmac, R = 0.1934 (Rfree = 0.000) for 4877 atoms. Found 23 (23 requested) and removed 18 (11 requested) atoms. Cycle 25: After refmac, R = 0.1936 (Rfree = 0.000) for 4864 atoms. Found 23 (23 requested) and removed 19 (11 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.87 3.67 Search for helices and strands: 0 residues in 0 chains, 5023 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 5038 seeds are put forward Round 1: 232 peptides, 49 chains. Longest chain 10 peptides. Score 0.254 Round 2: 265 peptides, 48 chains. Longest chain 14 peptides. Score 0.337 Round 3: 276 peptides, 45 chains. Longest chain 16 peptides. Score 0.386 Round 4: 272 peptides, 45 chains. Longest chain 15 peptides. Score 0.378 Round 5: 275 peptides, 44 chains. Longest chain 16 peptides. Score 0.393 Taking the results from Round 5 Chains 44, Residues 231, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6907 reflections ( 98.46 % complete ) and 12096 restraints for refining 5149 atoms. 11216 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2137 (Rfree = 0.000) for 5149 atoms. Found 24 (24 requested) and removed 27 (12 requested) atoms. Cycle 27: After refmac, R = 0.2172 (Rfree = 0.000) for 5108 atoms. Found 24 (24 requested) and removed 28 (12 requested) atoms. Cycle 28: After refmac, R = 0.2176 (Rfree = 0.000) for 5083 atoms. Found 24 (24 requested) and removed 27 (12 requested) atoms. Cycle 29: After refmac, R = 0.1735 (Rfree = 0.000) for 5042 atoms. Found 10 (24 requested) and removed 14 (12 requested) atoms. Cycle 30: After refmac, R = 0.1478 (Rfree = 0.000) for 5024 atoms. Found 3 (23 requested) and removed 15 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.86 3.66 Search for helices and strands: 0 residues in 0 chains, 5121 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 5134 seeds are put forward Round 1: 221 peptides, 51 chains. Longest chain 7 peptides. Score 0.209 Round 2: 251 peptides, 48 chains. Longest chain 10 peptides. Score 0.306 Round 3: 257 peptides, 44 chains. Longest chain 17 peptides. Score 0.356 Round 4: 257 peptides, 46 chains. Longest chain 11 peptides. Score 0.338 Round 5: 261 peptides, 46 chains. Longest chain 11 peptides. Score 0.346 Taking the results from Round 3 Chains 44, Residues 213, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6907 reflections ( 98.46 % complete ) and 11793 restraints for refining 5063 atoms. 10985 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2311 (Rfree = 0.000) for 5063 atoms. Found 24 (24 requested) and removed 31 (12 requested) atoms. Cycle 32: After refmac, R = 0.2064 (Rfree = 0.000) for 5033 atoms. Found 24 (24 requested) and removed 20 (12 requested) atoms. Cycle 33: After refmac, R = 0.2126 (Rfree = 0.000) for 5023 atoms. Found 23 (23 requested) and removed 17 (11 requested) atoms. Cycle 34: After refmac, R = 0.1950 (Rfree = 0.000) for 5012 atoms. Found 23 (23 requested) and removed 13 (11 requested) atoms. Cycle 35: After refmac, R = 0.1996 (Rfree = 0.000) for 5005 atoms. Found 23 (23 requested) and removed 15 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.92 3.72 Search for helices and strands: 0 residues in 0 chains, 5126 seeds are put forward NCS extension: 27 residues added (2 deleted due to clashes), 5153 seeds are put forward Round 1: 194 peptides, 44 chains. Longest chain 8 peptides. Score 0.213 Round 2: 221 peptides, 42 chains. Longest chain 9 peptides. Score 0.297 Round 3: 218 peptides, 40 chains. Longest chain 11 peptides. Score 0.310 Round 4: 211 peptides, 38 chains. Longest chain 10 peptides. Score 0.314 Round 5: 207 peptides, 39 chains. Longest chain 8 peptides. Score 0.295 Taking the results from Round 4 Chains 38, Residues 173, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6907 reflections ( 98.46 % complete ) and 11820 restraints for refining 5048 atoms. 11166 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2510 (Rfree = 0.000) for 5048 atoms. Found 23 (23 requested) and removed 33 (11 requested) atoms. Cycle 37: After refmac, R = 0.2284 (Rfree = 0.000) for 5010 atoms. Found 23 (23 requested) and removed 24 (11 requested) atoms. Cycle 38: After refmac, R = 0.2122 (Rfree = 0.000) for 4987 atoms. Found 23 (23 requested) and removed 14 (11 requested) atoms. Cycle 39: After refmac, R = 0.2102 (Rfree = 0.000) for 4983 atoms. Found 23 (23 requested) and removed 21 (11 requested) atoms. Cycle 40: After refmac, R = 0.2003 (Rfree = 0.000) for 4974 atoms. Found 19 (23 requested) and removed 17 (11 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.86 3.66 Search for helices and strands: 0 residues in 0 chains, 5089 seeds are put forward NCS extension: 10 residues added (2 deleted due to clashes), 5099 seeds are put forward Round 1: 166 peptides, 36 chains. Longest chain 8 peptides. Score 0.227 Round 2: 225 peptides, 45 chains. Longest chain 9 peptides. Score 0.277 Round 3: 224 peptides, 43 chains. Longest chain 11 peptides. Score 0.294 Round 4: 228 peptides, 43 chains. Longest chain 11 peptides. Score 0.303 Round 5: 224 peptides, 41 chains. Longest chain 13 peptides. Score 0.314 Taking the results from Round 5 Chains 41, Residues 183, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6907 reflections ( 98.46 % complete ) and 11517 restraints for refining 4983 atoms. 10826 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2395 (Rfree = 0.000) for 4983 atoms. Found 23 (23 requested) and removed 41 (11 requested) atoms. Cycle 42: After refmac, R = 0.2333 (Rfree = 0.000) for 4943 atoms. Found 23 (23 requested) and removed 22 (11 requested) atoms. Cycle 43: After refmac, R = 0.2031 (Rfree = 0.000) for 4930 atoms. Found 23 (23 requested) and removed 23 (11 requested) atoms. Cycle 44: After refmac, R = 0.2111 (Rfree = 0.000) for 4923 atoms. Found 23 (23 requested) and removed 16 (11 requested) atoms. Cycle 45: After refmac, R = 0.2004 (Rfree = 0.000) for 4915 atoms. Found 23 (23 requested) and removed 20 (11 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.82 3.62 Search for helices and strands: 0 residues in 0 chains, 5058 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 5070 seeds are put forward Round 1: 175 peptides, 38 chains. Longest chain 8 peptides. Score 0.228 Round 2: 193 peptides, 38 chains. Longest chain 9 peptides. Score 0.272 Round 3: 186 peptides, 37 chains. Longest chain 9 peptides. Score 0.266 Round 4: 195 peptides, 38 chains. Longest chain 9 peptides. Score 0.277 Round 5: 207 peptides, 40 chains. Longest chain 9 peptides. Score 0.285 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 40, Residues 167, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2fna-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6907 reflections ( 98.46 % complete ) and 11287 restraints for refining 4901 atoms. 10659 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2208 (Rfree = 0.000) for 4901 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 47: After refmac, R = 0.1971 (Rfree = 0.000) for 4863 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 48: After refmac, R = 0.2030 (Rfree = 0.000) for 4838 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 49: After refmac, R = 0.1980 (Rfree = 0.000) for 4819 atoms. Found 0 (22 requested) and removed 11 (11 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:31:19 GMT 2018 Job finished. TimeTaking 68.29 Used memory is bytes: 13216528