Sun 23 Dec 23:43:39 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2aml-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2aml-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2aml-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2aml-4.0-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/2aml-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2aml-4.0-parrot-mrncs ############### 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 23:43:43 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/mrncs/ArpWArp/wArpResults/WorkingDir/2aml-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2aml-4.0-parrot-mrncs/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-mrncs.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-mrncs.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 6595 atoms. Observations/parameters ratio is 0.23 ------------------------------------------------------ Starting model: R = 0.3378 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3196 (Rfree = 0.000) for 6595 atoms. Found 20 (31 requested) and removed 887 (15 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.77 4.26 Search for helices and strands: 0 residues in 0 chains, 5771 seeds are put forward NCS extension: 0 residues added, 5771 seeds are put forward Round 1: 140 peptides, 33 chains. Longest chain 6 peptides. Score 0.193 Round 2: 187 peptides, 36 chains. Longest chain 9 peptides. Score 0.294 Round 3: 199 peptides, 39 chains. Longest chain 11 peptides. Score 0.292 Round 4: 199 peptides, 37 chains. Longest chain 10 peptides. Score 0.315 Round 5: 193 peptides, 35 chains. Longest chain 11 peptides. Score 0.322 Taking the results from Round 5 Chains 35, Residues 158, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6170 reflections ( 99.66 % complete ) and 13417 restraints for refining 5390 atoms. 12820 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2933 (Rfree = 0.000) for 5390 atoms. Found 24 (25 requested) and removed 170 (12 requested) atoms. Cycle 2: After refmac, R = 0.2657 (Rfree = 0.000) for 5203 atoms. Found 24 (24 requested) and removed 58 (12 requested) atoms. Cycle 3: After refmac, R = 0.2499 (Rfree = 0.000) for 5133 atoms. Found 24 (24 requested) and removed 30 (12 requested) atoms. Cycle 4: After refmac, R = 0.2618 (Rfree = 0.000) for 5111 atoms. Found 24 (24 requested) and removed 31 (12 requested) atoms. Cycle 5: After refmac, R = 0.2481 (Rfree = 0.000) for 5083 atoms. Found 24 (24 requested) and removed 19 (12 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.69 4.17 Search for helices and strands: 0 residues in 0 chains, 5287 seeds are put forward NCS extension: 0 residues added, 5287 seeds are put forward Round 1: 177 peptides, 39 chains. Longest chain 8 peptides. Score 0.230 Round 2: 237 peptides, 45 chains. Longest chain 10 peptides. Score 0.325 Round 3: 266 peptides, 50 chains. Longest chain 11 peptides. Score 0.344 Round 4: 293 peptides, 53 chains. Longest chain 11 peptides. Score 0.378 Round 5: 305 peptides, 53 chains. Longest chain 13 peptides. Score 0.407 Taking the results from Round 5 Chains 53, Residues 252, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6170 reflections ( 99.66 % complete ) and 10632 restraints for refining 4712 atoms. 9677 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2339 (Rfree = 0.000) for 4712 atoms. Found 22 (22 requested) and removed 46 (11 requested) atoms. Cycle 7: After refmac, R = 0.2403 (Rfree = 0.000) for 4650 atoms. Found 22 (22 requested) and removed 36 (11 requested) atoms. Cycle 8: After refmac, R = 0.2312 (Rfree = 0.000) for 4598 atoms. Found 22 (22 requested) and removed 34 (11 requested) atoms. Cycle 9: After refmac, R = 0.2183 (Rfree = 0.000) for 4564 atoms. Found 21 (21 requested) and removed 26 (10 requested) atoms. Cycle 10: After refmac, R = 0.2236 (Rfree = 0.000) for 4537 atoms. Found 21 (21 requested) and removed 20 (10 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.70 4.18 Search for helices and strands: 0 residues in 0 chains, 4732 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 4747 seeds are put forward Round 1: 260 peptides, 52 chains. Longest chain 10 peptides. Score 0.308 Round 2: 302 peptides, 49 chains. Longest chain 18 peptides. Score 0.439 Round 3: 308 peptides, 50 chains. Longest chain 12 peptides. Score 0.443 Round 4: 319 peptides, 49 chains. Longest chain 15 peptides. Score 0.476 Round 5: 324 peptides, 53 chains. Longest chain 15 peptides. Score 0.449 Taking the results from Round 4 Chains 49, Residues 270, Estimated correctness of the model 0.0 % 2 chains (17 residues) have been docked in sequence ------------------------------------------------------ 6170 reflections ( 99.66 % complete ) and 10698 restraints for refining 4851 atoms. 9595 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2253 (Rfree = 0.000) for 4851 atoms. Found 23 (23 requested) and removed 42 (11 requested) atoms. Cycle 12: After refmac, R = 0.2174 (Rfree = 0.000) for 4798 atoms. Found 22 (22 requested) and removed 31 (11 requested) atoms. Cycle 13: After refmac, R = 0.2076 (Rfree = 0.000) for 4773 atoms. Found 22 (22 requested) and removed 32 (11 requested) atoms. Cycle 14: After refmac, R = 0.2003 (Rfree = 0.000) for 4756 atoms. Found 22 (22 requested) and removed 21 (11 requested) atoms. Cycle 15: After refmac, R = 0.1960 (Rfree = 0.000) for 4740 atoms. Found 22 (22 requested) and removed 19 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.67 4.14 Search for helices and strands: 0 residues in 0 chains, 4999 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 5014 seeds are put forward Round 1: 243 peptides, 50 chains. Longest chain 8 peptides. Score 0.286 Round 2: 298 peptides, 50 chains. Longest chain 13 peptides. Score 0.420 Round 3: 286 peptides, 50 chains. Longest chain 13 peptides. Score 0.392 Round 4: 288 peptides, 45 chains. Longest chain 20 peptides. Score 0.447 Round 5: 291 peptides, 49 chains. Longest chain 16 peptides. Score 0.414 Taking the results from Round 4 Chains 45, Residues 243, Estimated correctness of the model 0.0 % 1 chains (19 residues) have been docked in sequence ------------------------------------------------------ 6170 reflections ( 99.66 % complete ) and 11134 restraints for refining 4951 atoms. 10131 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1967 (Rfree = 0.000) for 4951 atoms. Found 20 (23 requested) and removed 51 (11 requested) atoms. Cycle 17: After refmac, R = 0.1921 (Rfree = 0.000) for 4895 atoms. Found 23 (23 requested) and removed 31 (11 requested) atoms. Cycle 18: After refmac, R = 0.1961 (Rfree = 0.000) for 4880 atoms. Found 23 (23 requested) and removed 20 (11 requested) atoms. Cycle 19: After refmac, R = 0.1955 (Rfree = 0.000) for 4868 atoms. Found 23 (23 requested) and removed 31 (11 requested) atoms. Cycle 20: After refmac, R = 0.1546 (Rfree = 0.000) for 4850 atoms. Found 5 (23 requested) and removed 21 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.71 4.19 Search for helices and strands: 0 residues in 0 chains, 5008 seeds are put forward NCS extension: 26 residues added (0 deleted due to clashes), 5034 seeds are put forward Round 1: 214 peptides, 46 chains. Longest chain 9 peptides. Score 0.253 Round 2: 274 peptides, 53 chains. Longest chain 9 peptides. Score 0.332 Round 3: 267 peptides, 48 chains. Longest chain 10 peptides. Score 0.367 Round 4: 258 peptides, 49 chains. Longest chain 12 peptides. Score 0.335 Round 5: 266 peptides, 48 chains. Longest chain 11 peptides. Score 0.365 Taking the results from Round 3 Chains 48, Residues 219, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6170 reflections ( 99.66 % complete ) and 11648 restraints for refining 4993 atoms. 10820 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1965 (Rfree = 0.000) for 4993 atoms. Found 23 (23 requested) and removed 42 (11 requested) atoms. Cycle 22: After refmac, R = 0.2043 (Rfree = 0.000) for 4949 atoms. Found 23 (23 requested) and removed 35 (11 requested) atoms. Cycle 23: After refmac, R = 0.1785 (Rfree = 0.000) for 4907 atoms. Found 20 (23 requested) and removed 20 (11 requested) atoms. Cycle 24: After refmac, R = 0.1530 (Rfree = 0.000) for 4894 atoms. Found 5 (23 requested) and removed 14 (11 requested) atoms. Cycle 25: After refmac, R = 0.1515 (Rfree = 0.000) for 4872 atoms. Found 13 (23 requested) and removed 17 (11 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.72 4.20 Search for helices and strands: 0 residues in 0 chains, 5061 seeds are put forward NCS extension: 7 residues added (2 deleted due to clashes), 5068 seeds are put forward Round 1: 210 peptides, 44 chains. Longest chain 12 peptides. Score 0.264 Round 2: 252 peptides, 45 chains. Longest chain 15 peptides. Score 0.362 Round 3: 245 peptides, 46 chains. Longest chain 12 peptides. Score 0.334 Round 4: 254 peptides, 46 chains. Longest chain 12 peptides. Score 0.357 Round 5: 232 peptides, 42 chains. Longest chain 12 peptides. Score 0.345 Taking the results from Round 2 Chains 45, Residues 207, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 6170 reflections ( 99.66 % complete ) and 11484 restraints for refining 4942 atoms. 10685 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1814 (Rfree = 0.000) for 4942 atoms. Found 23 (23 requested) and removed 31 (11 requested) atoms. Cycle 27: After refmac, R = 0.1904 (Rfree = 0.000) for 4919 atoms. Found 23 (23 requested) and removed 27 (11 requested) atoms. Cycle 28: After refmac, R = 0.1887 (Rfree = 0.000) for 4897 atoms. Found 23 (23 requested) and removed 20 (11 requested) atoms. Cycle 29: After refmac, R = 0.2009 (Rfree = 0.000) for 4880 atoms. Found 23 (23 requested) and removed 23 (11 requested) atoms. Cycle 30: After refmac, R = 0.2015 (Rfree = 0.000) for 4863 atoms. Found 23 (23 requested) and removed 27 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.74 4.22 Search for helices and strands: 0 residues in 0 chains, 5043 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 5058 seeds are put forward Round 1: 163 peptides, 34 chains. Longest chain 7 peptides. Score 0.251 Round 2: 227 peptides, 44 chains. Longest chain 14 peptides. Score 0.310 Round 3: 219 peptides, 41 chains. Longest chain 10 peptides. Score 0.322 Round 4: 215 peptides, 38 chains. Longest chain 10 peptides. Score 0.345 Round 5: 227 peptides, 42 chains. Longest chain 11 peptides. Score 0.332 Taking the results from Round 4 Chains 38, Residues 177, Estimated correctness of the model 0.0 % 2 chains (11 residues) have been docked in sequence ------------------------------------------------------ 6170 reflections ( 99.66 % complete ) and 11215 restraints for refining 4883 atoms. 10503 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2058 (Rfree = 0.000) for 4883 atoms. Found 23 (23 requested) and removed 39 (11 requested) atoms. Cycle 32: After refmac, R = 0.2175 (Rfree = 0.000) for 4851 atoms. Found 23 (23 requested) and removed 26 (11 requested) atoms. Cycle 33: After refmac, R = 0.2050 (Rfree = 0.000) for 4833 atoms. Found 23 (23 requested) and removed 58 (11 requested) atoms. Cycle 34: After refmac, R = 0.2092 (Rfree = 0.000) for 4781 atoms. Found 22 (22 requested) and removed 35 (11 requested) atoms. Cycle 35: After refmac, R = 0.2086 (Rfree = 0.000) for 4755 atoms. Found 22 (22 requested) and removed 31 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.75 4.23 Search for helices and strands: 0 residues in 0 chains, 4922 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 4934 seeds are put forward Round 1: 184 peptides, 41 chains. Longest chain 8 peptides. Score 0.227 Round 2: 208 peptides, 40 chains. Longest chain 8 peptides. Score 0.305 Round 3: 220 peptides, 38 chains. Longest chain 22 peptides. Score 0.358 Round 4: 226 peptides, 38 chains. Longest chain 15 peptides. Score 0.373 Round 5: 221 peptides, 39 chains. Longest chain 16 peptides. Score 0.350 Taking the results from Round 4 Chains 38, Residues 188, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 6170 reflections ( 99.66 % complete ) and 10610 restraints for refining 4645 atoms. 9875 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2045 (Rfree = 0.000) for 4645 atoms. Found 22 (22 requested) and removed 87 (11 requested) atoms. Cycle 37: After refmac, R = 0.1892 (Rfree = 0.000) for 4562 atoms. Found 21 (21 requested) and removed 33 (10 requested) atoms. Cycle 38: After refmac, R = 0.1971 (Rfree = 0.000) for 4538 atoms. Found 21 (21 requested) and removed 18 (10 requested) atoms. Cycle 39: After refmac, R = 0.1864 (Rfree = 0.000) for 4531 atoms. Found 21 (21 requested) and removed 13 (10 requested) atoms. Cycle 40: After refmac, R = 0.1527 (Rfree = 0.000) for 4530 atoms. Found 2 (21 requested) and removed 18 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.74 4.22 Search for helices and strands: 0 residues in 0 chains, 4652 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 4675 seeds are put forward Round 1: 184 peptides, 38 chains. Longest chain 9 peptides. Score 0.262 Round 2: 179 peptides, 35 chains. Longest chain 12 peptides. Score 0.284 Round 3: 183 peptides, 35 chains. Longest chain 10 peptides. Score 0.295 Round 4: 192 peptides, 37 chains. Longest chain 9 peptides. Score 0.296 Round 5: 172 peptides, 30 chains. Longest chain 12 peptides. Score 0.325 Taking the results from Round 5 Chains 30, Residues 142, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6170 reflections ( 99.66 % complete ) and 10886 restraints for refining 4612 atoms. 10348 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1968 (Rfree = 0.000) for 4612 atoms. Found 21 (21 requested) and removed 40 (10 requested) atoms. Cycle 42: After refmac, R = 0.2103 (Rfree = 0.000) for 4576 atoms. Found 21 (21 requested) and removed 43 (10 requested) atoms. Cycle 43: After refmac, R = 0.1974 (Rfree = 0.000) for 4543 atoms. Found 21 (21 requested) and removed 54 (10 requested) atoms. Cycle 44: After refmac, R = 0.2270 (Rfree = 0.000) for 4503 atoms. Found 21 (21 requested) and removed 26 (10 requested) atoms. Cycle 45: After refmac, R = 0.2079 (Rfree = 0.000) for 4489 atoms. Found 21 (21 requested) and removed 45 (10 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.69 4.17 Search for helices and strands: 0 residues in 0 chains, 4618 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 4635 seeds are put forward Round 1: 145 peptides, 34 chains. Longest chain 6 peptides. Score 0.196 Round 2: 170 peptides, 35 chains. Longest chain 8 peptides. Score 0.259 Round 3: 166 peptides, 33 chains. Longest chain 9 peptides. Score 0.272 Round 4: 164 peptides, 32 chains. Longest chain 8 peptides. Score 0.278 Round 5: 169 peptides, 34 chains. Longest chain 9 peptides. Score 0.268 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 32, Residues 132, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence Sequence coverage is 5 % 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 10231 restraints for refining 4490 atoms. 9706 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2046 (Rfree = 0.000) for 4490 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. Cycle 47: After refmac, R = 0.2080 (Rfree = 0.000) for 4463 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. Cycle 48: After refmac, R = 0.2150 (Rfree = 0.000) for 4443 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. Cycle 49: After refmac, R = 0.2007 (Rfree = 0.000) for 4425 atoms. TimeTaking 50.4