Mon 24 Dec 07:37:24 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2aml-4.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2aml-4.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2aml-4.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2aml-4.0-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2aml-4.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2aml-4.0-parrot-noncs ############### 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 ============================================================ Mon 24 Dec 07:37:29 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/noncs/ArpWArp/wArpResults/WorkingDir/2aml-4.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2aml-4.0-parrot-noncs/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 428 and 0 Target number of residues in the AU: 428 Target solvent content: 0.6624 Checking the provided sequence file Detected sequence length: 373 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 746 Adjusted target solvent content: 0.41 Input MTZ file: 2aml-4.0-parrot-noncs.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: 19 Cell parameters: 56.315 101.397 120.151 90.000 90.000 90.000 Input sequence file: 2aml-4.0-parrot-noncs.fasta_lf Building free atoms model in initial map for 5968 target number of atoms Had to go as low as 0.65 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: 77.491 4.000 Wilson plot Bfac: 86.49 6170 reflections ( 99.66 % complete ) and 0 restraints for refining 6592 atoms. Observations/parameters ratio is 0.23 ------------------------------------------------------ Starting model: R = 0.3509 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3578 (Rfree = 0.000) for 6592 atoms. Found 31 (31 requested) and removed 257 (15 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.57 4.03 Search for helices and strands: 0 residues in 0 chains, 6424 seeds are put forward NCS extension: 0 residues added, 6424 seeds are put forward Round 1: 127 peptides, 30 chains. Longest chain 7 peptides. Score 0.190 Round 2: 179 peptides, 38 chains. Longest chain 9 peptides. Score 0.248 Round 3: 214 peptides, 44 chains. Longest chain 8 peptides. Score 0.275 Round 4: 213 peptides, 39 chains. Longest chain 10 peptides. Score 0.329 Round 5: 220 peptides, 42 chains. Longest chain 10 peptides. Score 0.314 Taking the results from Round 4 Chains 39, Residues 174, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 6170 reflections ( 99.66 % complete ) and 13537 restraints for refining 5388 atoms. 12865 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2748 (Rfree = 0.000) for 5388 atoms. Found 25 (25 requested) and removed 72 (12 requested) atoms. Cycle 2: After refmac, R = 0.2772 (Rfree = 0.000) for 5277 atoms. Found 25 (25 requested) and removed 45 (12 requested) atoms. Cycle 3: After refmac, R = 0.2719 (Rfree = 0.000) for 5215 atoms. Found 24 (24 requested) and removed 51 (12 requested) atoms. Cycle 4: After refmac, R = 0.2546 (Rfree = 0.000) for 5162 atoms. Found 22 (24 requested) and removed 40 (12 requested) atoms. Cycle 5: After refmac, R = 0.2490 (Rfree = 0.000) for 5122 atoms. Found 24 (24 requested) and removed 33 (12 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.73 4.21 Search for helices and strands: 0 residues in 0 chains, 5302 seeds are put forward NCS extension: 3 residues added (0 deleted due to clashes), 5305 seeds are put forward Round 1: 212 peptides, 50 chains. Longest chain 7 peptides. Score 0.201 Round 2: 266 peptides, 53 chains. Longest chain 16 peptides. Score 0.312 Round 3: 285 peptides, 53 chains. Longest chain 11 peptides. Score 0.359 Round 4: 294 peptides, 54 chains. Longest chain 13 peptides. Score 0.371 Round 5: 291 peptides, 52 chains. Longest chain 12 peptides. Score 0.384 Taking the results from Round 5 Chains 52, Residues 239, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 6170 reflections ( 99.66 % complete ) and 11342 restraints for refining 4942 atoms. 10412 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2433 (Rfree = 0.000) for 4942 atoms. Found 23 (23 requested) and removed 98 (11 requested) atoms. Cycle 7: After refmac, R = 0.2334 (Rfree = 0.000) for 4817 atoms. Found 23 (23 requested) and removed 52 (11 requested) atoms. Cycle 8: After refmac, R = 0.2254 (Rfree = 0.000) for 4762 atoms. Found 22 (22 requested) and removed 44 (11 requested) atoms. Cycle 9: After refmac, R = 0.2198 (Rfree = 0.000) for 4719 atoms. Found 22 (22 requested) and removed 42 (11 requested) atoms. Cycle 10: After refmac, R = 0.2214 (Rfree = 0.000) for 4672 atoms. Found 22 (22 requested) and removed 32 (11 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.70 4.18 Search for helices and strands: 0 residues in 0 chains, 4858 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 4872 seeds are put forward Round 1: 224 peptides, 45 chains. Longest chain 10 peptides. Score 0.291 Round 2: 272 peptides, 50 chains. Longest chain 12 peptides. Score 0.359 Round 3: 281 peptides, 49 chains. Longest chain 14 peptides. Score 0.391 Round 4: 275 peptides, 47 chains. Longest chain 13 peptides. Score 0.397 Round 5: 281 peptides, 45 chains. Longest chain 16 peptides. Score 0.431 Taking the results from Round 5 Chains 45, Residues 236, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6170 reflections ( 99.66 % complete ) and 11193 restraints for refining 4908 atoms. 10294 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2145 (Rfree = 0.000) for 4908 atoms. Found 21 (23 requested) and removed 78 (11 requested) atoms. Cycle 12: After refmac, R = 0.2101 (Rfree = 0.000) for 4814 atoms. Found 23 (23 requested) and removed 37 (11 requested) atoms. Cycle 13: After refmac, R = 0.2358 (Rfree = 0.000) for 4779 atoms. Found 22 (22 requested) and removed 50 (11 requested) atoms. Cycle 14: After refmac, R = 0.2017 (Rfree = 0.000) for 4723 atoms. Found 22 (22 requested) and removed 31 (11 requested) atoms. Cycle 15: After refmac, R = 0.2009 (Rfree = 0.000) for 4690 atoms. Found 22 (22 requested) and removed 21 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.73 4.21 Search for helices and strands: 0 residues in 0 chains, 4919 seeds are put forward NCS extension: 26 residues added (0 deleted due to clashes), 4945 seeds are put forward Round 1: 196 peptides, 43 chains. Longest chain 9 peptides. Score 0.237 Round 2: 272 peptides, 52 chains. Longest chain 9 peptides. Score 0.338 Round 3: 266 peptides, 46 chains. Longest chain 11 peptides. Score 0.386 Round 4: 259 peptides, 43 chains. Longest chain 13 peptides. Score 0.400 Round 5: 275 peptides, 48 chains. Longest chain 12 peptides. Score 0.387 Taking the results from Round 4 Chains 43, Residues 216, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6170 reflections ( 99.66 % complete ) and 11143 restraints for refining 4803 atoms. 10322 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2022 (Rfree = 0.000) for 4803 atoms. Found 22 (22 requested) and removed 50 (11 requested) atoms. Cycle 17: After refmac, R = 0.1952 (Rfree = 0.000) for 4753 atoms. Found 22 (22 requested) and removed 35 (11 requested) atoms. Cycle 18: After refmac, R = 0.2027 (Rfree = 0.000) for 4724 atoms. Found 22 (22 requested) and removed 30 (11 requested) atoms. Cycle 19: After refmac, R = 0.1833 (Rfree = 0.000) for 4709 atoms. Found 22 (22 requested) and removed 25 (11 requested) atoms. Cycle 20: After refmac, R = 0.1865 (Rfree = 0.000) for 4696 atoms. Found 22 (22 requested) and removed 19 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.71 4.19 Search for helices and strands: 0 residues in 0 chains, 4877 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 4898 seeds are put forward Round 1: 216 peptides, 44 chains. Longest chain 8 peptides. Score 0.281 Round 2: 285 peptides, 53 chains. Longest chain 11 peptides. Score 0.359 Round 3: 287 peptides, 48 chains. Longest chain 11 peptides. Score 0.415 Round 4: 283 peptides, 48 chains. Longest chain 16 peptides. Score 0.405 Round 5: 295 peptides, 52 chains. Longest chain 11 peptides. Score 0.393 Taking the results from Round 3 Chains 48, Residues 239, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 6170 reflections ( 99.66 % complete ) and 11177 restraints for refining 4916 atoms. 10269 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1757 (Rfree = 0.000) for 4916 atoms. Found 23 (23 requested) and removed 27 (11 requested) atoms. Cycle 22: After refmac, R = 0.1793 (Rfree = 0.000) for 4881 atoms. Found 23 (23 requested) and removed 30 (11 requested) atoms. Cycle 23: After refmac, R = 0.1315 (Rfree = 0.000) for 4855 atoms. Found 5 (23 requested) and removed 18 (11 requested) atoms. Cycle 24: After refmac, R = 0.1583 (Rfree = 0.000) for 4836 atoms. Found 23 (23 requested) and removed 27 (11 requested) atoms. Cycle 25: After refmac, R = 0.1263 (Rfree = 0.000) for 4827 atoms. Found 9 (22 requested) and removed 23 (11 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.73 4.21 Search for helices and strands: 0 residues in 0 chains, 4967 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 4980 seeds are put forward Round 1: 242 peptides, 52 chains. Longest chain 10 peptides. Score 0.261 Round 2: 270 peptides, 52 chains. Longest chain 10 peptides. Score 0.333 Round 3: 271 peptides, 49 chains. Longest chain 10 peptides. Score 0.367 Round 4: 284 peptides, 48 chains. Longest chain 12 peptides. Score 0.408 Round 5: 260 peptides, 45 chains. Longest chain 14 peptides. Score 0.382 Taking the results from Round 4 Chains 48, Residues 236, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 6170 reflections ( 99.66 % complete ) and 11836 restraints for refining 5038 atoms. 10925 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1896 (Rfree = 0.000) for 5038 atoms. Found 23 (23 requested) and removed 54 (11 requested) atoms. Cycle 27: After refmac, R = 0.1960 (Rfree = 0.000) for 4992 atoms. Found 23 (23 requested) and removed 37 (11 requested) atoms. Cycle 28: After refmac, R = 0.1989 (Rfree = 0.000) for 4969 atoms. Found 23 (23 requested) and removed 29 (11 requested) atoms. Cycle 29: After refmac, R = 0.1860 (Rfree = 0.000) for 4956 atoms. Found 23 (23 requested) and removed 25 (11 requested) atoms. Cycle 30: After refmac, R = 0.1911 (Rfree = 0.000) for 4943 atoms. Found 23 (23 requested) and removed 27 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.76 4.24 Search for helices and strands: 0 residues in 0 chains, 5107 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 5123 seeds are put forward Round 1: 226 peptides, 50 chains. Longest chain 9 peptides. Score 0.240 Round 2: 251 peptides, 49 chains. Longest chain 12 peptides. Score 0.317 Round 3: 257 peptides, 48 chains. Longest chain 11 peptides. Score 0.343 Round 4: 267 peptides, 45 chains. Longest chain 14 peptides. Score 0.398 Round 5: 267 peptides, 43 chains. Longest chain 14 peptides. Score 0.419 Taking the results from Round 5 Chains 43, Residues 224, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6170 reflections ( 99.66 % complete ) and 12129 restraints for refining 5124 atoms. 11276 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1869 (Rfree = 0.000) for 5124 atoms. Found 18 (24 requested) and removed 46 (12 requested) atoms. Cycle 32: After refmac, R = 0.2098 (Rfree = 0.000) for 5075 atoms. Found 24 (24 requested) and removed 30 (12 requested) atoms. Cycle 33: After refmac, R = 0.2060 (Rfree = 0.000) for 5061 atoms. Found 24 (24 requested) and removed 32 (12 requested) atoms. Cycle 34: After refmac, R = 0.1888 (Rfree = 0.000) for 5043 atoms. Found 24 (24 requested) and removed 27 (12 requested) atoms. Cycle 35: After refmac, R = 0.2060 (Rfree = 0.000) for 5029 atoms. Found 23 (23 requested) and removed 27 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.72 4.20 Search for helices and strands: 0 residues in 0 chains, 5199 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 5221 seeds are put forward Round 1: 190 peptides, 44 chains. Longest chain 7 peptides. Score 0.208 Round 2: 217 peptides, 43 chains. Longest chain 11 peptides. Score 0.295 Round 3: 218 peptides, 44 chains. Longest chain 11 peptides. Score 0.286 Round 4: 220 peptides, 43 chains. Longest chain 11 peptides. Score 0.303 Round 5: 205 peptides, 39 chains. Longest chain 11 peptides. Score 0.308 Taking the results from Round 5 Chains 39, Residues 166, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 6170 reflections ( 99.66 % complete ) and 12387 restraints for refining 5122 atoms. 11738 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2095 (Rfree = 0.000) for 5122 atoms. Found 24 (24 requested) and removed 55 (12 requested) atoms. Cycle 37: After refmac, R = 0.2059 (Rfree = 0.000) for 5079 atoms. Found 24 (24 requested) and removed 25 (12 requested) atoms. Cycle 38: After refmac, R = 0.2246 (Rfree = 0.000) for 5058 atoms. Found 24 (24 requested) and removed 27 (12 requested) atoms. Failed to save intermediate PDB Cycle 39: After refmac, R = 0.2007 (Rfree = 0.000) for 5041 atoms. Found 24 (24 requested) and removed 18 (12 requested) atoms. Cycle 40: After refmac, R = 0.1630 (Rfree = 0.000) for 5042 atoms. Found 6 (23 requested) and removed 19 (11 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.73 4.21 Search for helices and strands: 0 residues in 0 chains, 5191 seeds are put forward NCS extension: 5 residues added (1 deleted due to clashes), 5196 seeds are put forward Round 1: 143 peptides, 32 chains. Longest chain 7 peptides. Score 0.215 Round 2: 166 peptides, 34 chains. Longest chain 8 peptides. Score 0.259 Round 3: 197 peptides, 38 chains. Longest chain 11 peptides. Score 0.298 Round 4: 176 peptides, 35 chains. Longest chain 10 peptides. Score 0.276 Round 5: 169 peptides, 32 chains. Longest chain 11 peptides. Score 0.292 Taking the results from Round 3 Chains 38, Residues 159, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6170 reflections ( 99.66 % complete ) and 12197 restraints for refining 5001 atoms. 11599 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2168 (Rfree = 0.000) for 5001 atoms. Found 23 (23 requested) and removed 33 (11 requested) atoms. Cycle 42: After refmac, R = 0.2219 (Rfree = 0.000) for 4975 atoms. Found 23 (23 requested) and removed 48 (11 requested) atoms. Cycle 43: After refmac, R = 0.2255 (Rfree = 0.000) for 4935 atoms. Found 23 (23 requested) and removed 29 (11 requested) atoms. Cycle 44: After refmac, R = 0.2105 (Rfree = 0.000) for 4918 atoms. Found 23 (23 requested) and removed 20 (11 requested) atoms. Cycle 45: After refmac, R = 0.2308 (Rfree = 0.000) for 4912 atoms. Found 23 (23 requested) and removed 34 (11 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.75 4.23 Search for helices and strands: 0 residues in 0 chains, 5055 seeds are put forward NCS extension: 10 residues added (2 deleted due to clashes), 5065 seeds are put forward Round 1: 119 peptides, 29 chains. Longest chain 6 peptides. Score 0.177 Round 2: 173 peptides, 38 chains. Longest chain 6 peptides. Score 0.231 Round 3: 156 peptides, 32 chains. Longest chain 7 peptides. Score 0.255 Round 4: 166 peptides, 34 chains. Longest chain 11 peptides. Score 0.259 Round 5: 153 peptides, 32 chains. Longest chain 8 peptides. Score 0.246 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 34, Residues 132, 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 2aml-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6170 reflections ( 99.66 % complete ) and 11114 restraints for refining 4706 atoms. 10620 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2179 (Rfree = 0.000) for 4706 atoms. Found 0 (22 requested) and removed 11 (11 requested) atoms. Cycle 47: After refmac, R = 0.2168 (Rfree = 0.000) for 4684 atoms. Found 0 (22 requested) and removed 11 (11 requested) atoms. Cycle 48: After refmac, R = 0.2064 (Rfree = 0.000) for 4664 atoms. Found 0 (22 requested) and removed 11 (11 requested) atoms. Cycle 49: After refmac, R = 0.2031 (Rfree = 0.000) for 4643 atoms. TimeTaking 49.37