null Mon 24 Dec 07:56:29 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 2aam-3.2-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2aam-3.2-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2aam-3.2-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2aam-3.2-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/2aam-3.2-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2aam-3.2-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 07:56:34 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/2aam-3.2-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2aam-3.2-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 4070 and 0 Target number of residues in the AU: 4070 Target solvent content: 0.6050 Target number of residues exceeds 1700, conditional restraints are disabled Checking the provided sequence file Detected sequence length: 309 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 6 Adjusted target number of residues: 1854 Adjusted target solvent content: 0.82 Input MTZ file: 2aam-3.2-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: 4 Cell parameters: 195.000 84.610 194.910 90.000 119.891 90.000 Input sequence file: 2aam-3.2-parrot-noncs.fasta_lf Building free atoms model in initial map for 14832 target number of atoms Had to go as low as 1.50 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. 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: 169.060 3.200 Wilson plot Bfac: 54.68 90855 reflections ( 99.15 % complete ) and 0 restraints for refining 16678 atoms. Observations/parameters ratio is 1.36 ------------------------------------------------------ Starting model: R = 0.3536 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2757 (Rfree = 0.000) for 16678 atoms. Found 149 (149 requested) and removed 91 (74 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.05 1.84 Search for helices and strands: 0 residues in 0 chains, 17064 seeds are put forward NCS extension: 0 residues added, 17064 seeds are put forward Round 1: 1322 peptides, 157 chains. Longest chain 28 peptides. Score 0.428 Round 2: 1361 peptides, 157 chains. Longest chain 24 peptides. Score 0.440 Round 3: 1348 peptides, 157 chains. Longest chain 26 peptides. Score 0.436 Round 4: 1377 peptides, 155 chains. Longest chain 32 peptides. Score 0.448 Round 5: 1368 peptides, 163 chains. Longest chain 27 peptides. Score 0.433 Taking the results from Round 4 Chains 160, Residues 1222, Estimated correctness of the model 0.0 % 8 chains (111 residues) have been docked in sequence ------------------------------------------------------ 90855 reflections ( 99.15 % complete ) and 5203 restraints for refining 16000 atoms. Observations/parameters ratio is 1.42 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2637 (Rfree = 0.000) for 16000 atoms. Found 143 (143 requested) and removed 79 (71 requested) atoms. Cycle 2: After refmac, R = 0.2465 (Rfree = 0.000) for 16064 atoms. Found 144 (144 requested) and removed 73 (72 requested) atoms. Cycle 3: After refmac, R = 0.2383 (Rfree = 0.000) for 16135 atoms. Found 71 (144 requested) and removed 75 (72 requested) atoms. Cycle 4: After refmac, R = 0.2351 (Rfree = 0.000) for 16131 atoms. Found 50 (144 requested) and removed 75 (72 requested) atoms. Cycle 5: After refmac, R = 0.2309 (Rfree = 0.000) for 16106 atoms. Found 50 (144 requested) and removed 77 (72 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.05 1.84 Search for helices and strands: 0 residues in 0 chains, 16606 seeds are put forward NCS extension: 15 residues added (8 deleted due to clashes), 16621 seeds are put forward Round 1: 1421 peptides, 160 chains. Longest chain 41 peptides. Score 0.453 Round 2: 1407 peptides, 156 chains. Longest chain 26 peptides. Score 0.455 Round 3: 1423 peptides, 163 chains. Longest chain 27 peptides. Score 0.450 Round 4: 1416 peptides, 156 chains. Longest chain 32 peptides. Score 0.457 Round 5: 1394 peptides, 164 chains. Longest chain 26 peptides. Score 0.440 Taking the results from Round 4 Chains 166, Residues 1260, Estimated correctness of the model 0.0 % 13 chains (220 residues) have been docked in sequence ------------------------------------------------------ 90855 reflections ( 99.15 % complete ) and 5878 restraints for refining 16370 atoms. Observations/parameters ratio is 1.39 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2497 (Rfree = 0.000) for 16370 atoms. Found 146 (146 requested) and removed 93 (73 requested) atoms. Cycle 7: After refmac, R = 0.2314 (Rfree = 0.000) for 16423 atoms. Found 86 (147 requested) and removed 81 (73 requested) atoms. Cycle 8: After refmac, R = 0.2228 (Rfree = 0.000) for 16428 atoms. Found 46 (147 requested) and removed 78 (73 requested) atoms. Cycle 9: After refmac, R = 0.2195 (Rfree = 0.000) for 16396 atoms. Found 37 (147 requested) and removed 75 (73 requested) atoms. Cycle 10: After refmac, R = 0.2194 (Rfree = 0.000) for 16358 atoms. Found 60 (146 requested) and removed 79 (73 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.07 1.85 Search for helices and strands: 0 residues in 0 chains, 16831 seeds are put forward NCS extension: 20 residues added (6 deleted due to clashes), 16851 seeds are put forward Round 1: 1414 peptides, 157 chains. Longest chain 36 peptides. Score 0.455 Round 2: 1407 peptides, 168 chains. Longest chain 27 peptides. Score 0.438 Round 3: 1408 peptides, 164 chains. Longest chain 28 peptides. Score 0.444 Round 4: 1423 peptides, 160 chains. Longest chain 32 peptides. Score 0.454 Round 5: 1395 peptides, 154 chains. Longest chain 30 peptides. Score 0.454 Taking the results from Round 1 Chains 171, Residues 1257, Estimated correctness of the model 0.0 % 13 chains (156 residues) have been docked in sequence ------------------------------------------------------ 90855 reflections ( 99.15 % complete ) and 5618 restraints for refining 16050 atoms. Observations/parameters ratio is 1.42 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2354 (Rfree = 0.000) for 16050 atoms. Found 144 (144 requested) and removed 77 (72 requested) atoms. Cycle 12: After refmac, R = 0.2228 (Rfree = 0.000) for 16117 atoms. Found 101 (144 requested) and removed 77 (72 requested) atoms. Cycle 13: After refmac, R = 0.2184 (Rfree = 0.000) for 16141 atoms. Found 57 (144 requested) and removed 75 (72 requested) atoms. Cycle 14: After refmac, R = 0.2153 (Rfree = 0.000) for 16123 atoms. Found 64 (144 requested) and removed 75 (72 requested) atoms. Cycle 15: After refmac, R = 0.2141 (Rfree = 0.000) for 16112 atoms. Found 65 (144 requested) and removed 76 (72 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.08 1.86 Search for helices and strands: 0 residues in 0 chains, 16600 seeds are put forward NCS extension: 28 residues added (6 deleted due to clashes), 16628 seeds are put forward Round 1: 1405 peptides, 166 chains. Longest chain 33 peptides. Score 0.440 Round 2: 1462 peptides, 161 chains. Longest chain 35 peptides. Score 0.464 Round 3: 1479 peptides, 161 chains. Longest chain 36 peptides. Score 0.468 Round 4: 1450 peptides, 150 chains. Longest chain 40 peptides. Score 0.475 Round 5: 1444 peptides, 151 chains. Longest chain 41 peptides. Score 0.472 Taking the results from Round 4 Chains 156, Residues 1300, Estimated correctness of the model 3.1 % 9 chains (181 residues) have been docked in sequence ------------------------------------------------------ 90855 reflections ( 99.15 % complete ) and 5894 restraints for refining 16538 atoms. Observations/parameters ratio is 1.37 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2359 (Rfree = 0.000) for 16538 atoms. Found 148 (148 requested) and removed 90 (74 requested) atoms. Cycle 17: After refmac, R = 0.2193 (Rfree = 0.000) for 16596 atoms. Found 108 (148 requested) and removed 82 (74 requested) atoms. Cycle 18: After refmac, R = 0.2127 (Rfree = 0.000) for 16622 atoms. Found 51 (149 requested) and removed 77 (74 requested) atoms. Cycle 19: After refmac, R = 0.2114 (Rfree = 0.000) for 16596 atoms. Found 48 (148 requested) and removed 77 (74 requested) atoms. Cycle 20: After refmac, R = 0.2105 (Rfree = 0.000) for 16567 atoms. Found 57 (148 requested) and removed 76 (74 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.06 1.85 Search for helices and strands: 0 residues in 0 chains, 16960 seeds are put forward NCS extension: 28 residues added (6 deleted due to clashes), 16988 seeds are put forward Round 1: 1480 peptides, 181 chains. Longest chain 48 peptides. Score 0.441 Round 2: 1505 peptides, 161 chains. Longest chain 51 peptides. Score 0.476 Round 3: 1463 peptides, 148 chains. Longest chain 38 peptides. Score 0.482 Round 4: 1444 peptides, 150 chains. Longest chain 36 peptides. Score 0.474 Round 5: 1457 peptides, 160 chains. Longest chain 29 peptides. Score 0.464 Taking the results from Round 3 Chains 159, Residues 1315, Estimated correctness of the model 5.4 % 12 chains (222 residues) have been docked in sequence ------------------------------------------------------ 90855 reflections ( 99.15 % complete ) and 6131 restraints for refining 16834 atoms. Observations/parameters ratio is 1.35 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2363 (Rfree = 0.000) for 16834 atoms. Found 151 (151 requested) and removed 95 (75 requested) atoms. Cycle 22: After refmac, R = 0.2226 (Rfree = 0.000) for 16890 atoms. Found 118 (151 requested) and removed 79 (75 requested) atoms. Cycle 23: After refmac, R = 0.2170 (Rfree = 0.000) for 16929 atoms. Found 46 (151 requested) and removed 78 (75 requested) atoms. Cycle 24: After refmac, R = 0.2170 (Rfree = 0.000) for 16897 atoms. Found 50 (151 requested) and removed 77 (75 requested) atoms. Cycle 25: After refmac, R = 0.2156 (Rfree = 0.000) for 16870 atoms. Found 55 (151 requested) and removed 78 (75 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.05 1.84 Search for helices and strands: 0 residues in 0 chains, 17312 seeds are put forward NCS extension: 30 residues added (8 deleted due to clashes), 17342 seeds are put forward Round 1: 1406 peptides, 159 chains. Longest chain 40 peptides. Score 0.450 Round 2: 1435 peptides, 156 chains. Longest chain 34 peptides. Score 0.463 Round 3: 1479 peptides, 155 chains. Longest chain 54 peptides. Score 0.477 Round 4: 1467 peptides, 152 chains. Longest chain 43 peptides. Score 0.477 Round 5: 1461 peptides, 157 chains. Longest chain 49 peptides. Score 0.469 Taking the results from Round 4 Chains 159, Residues 1315, Estimated correctness of the model 3.7 % 12 chains (197 residues) have been docked in sequence ------------------------------------------------------ 90855 reflections ( 99.15 % complete ) and 5954 restraints for refining 16808 atoms. Observations/parameters ratio is 1.35 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2327 (Rfree = 0.000) for 16808 atoms. Found 150 (150 requested) and removed 92 (75 requested) atoms. Cycle 27: After refmac, R = 0.2156 (Rfree = 0.000) for 16866 atoms. Found 98 (151 requested) and removed 76 (75 requested) atoms. Cycle 28: After refmac, R = 0.2080 (Rfree = 0.000) for 16888 atoms. Found 59 (151 requested) and removed 76 (75 requested) atoms. Cycle 29: After refmac, R = 0.2050 (Rfree = 0.000) for 16871 atoms. Found 47 (151 requested) and removed 76 (75 requested) atoms. Cycle 30: After refmac, R = 0.2039 (Rfree = 0.000) for 16842 atoms. Found 39 (151 requested) and removed 77 (75 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.04 1.83 Search for helices and strands: 0 residues in 0 chains, 17250 seeds are put forward NCS extension: 25 residues added (12 deleted due to clashes), 17275 seeds are put forward Round 1: 1408 peptides, 157 chains. Longest chain 40 peptides. Score 0.454 Round 2: 1491 peptides, 156 chains. Longest chain 44 peptides. Score 0.478 Round 3: 1489 peptides, 160 chains. Longest chain 48 peptides. Score 0.472 Round 4: 1477 peptides, 152 chains. Longest chain 51 peptides. Score 0.480 Round 5: 1470 peptides, 167 chains. Longest chain 39 peptides. Score 0.457 Taking the results from Round 4 Chains 164, Residues 1325, Estimated correctness of the model 4.7 % 15 chains (268 residues) have been docked in sequence ------------------------------------------------------ 90855 reflections ( 99.15 % complete ) and 6365 restraints for refining 16879 atoms. Observations/parameters ratio is 1.35 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2319 (Rfree = 0.000) for 16879 atoms. Found 151 (151 requested) and removed 87 (75 requested) atoms. Cycle 32: After refmac, R = 0.2160 (Rfree = 0.000) for 16943 atoms. Found 106 (152 requested) and removed 78 (76 requested) atoms. Cycle 33: After refmac, R = 0.2091 (Rfree = 0.000) for 16971 atoms. Found 51 (152 requested) and removed 79 (76 requested) atoms. Cycle 34: After refmac, R = 0.2055 (Rfree = 0.000) for 16943 atoms. Found 40 (152 requested) and removed 77 (76 requested) atoms. Cycle 35: After refmac, R = 0.2036 (Rfree = 0.000) for 16906 atoms. Found 34 (151 requested) and removed 77 (75 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.04 1.83 Search for helices and strands: 0 residues in 0 chains, 17309 seeds are put forward NCS extension: 16 residues added (9 deleted due to clashes), 17325 seeds are put forward Round 1: 1400 peptides, 157 chains. Longest chain 48 peptides. Score 0.451 Round 2: 1474 peptides, 151 chains. Longest chain 39 peptides. Score 0.481 Round 3: 1462 peptides, 139 chains. Longest chain 50 peptides. Score 0.494 Round 4: 1432 peptides, 151 chains. Longest chain 46 peptides. Score 0.469 Round 5: 1438 peptides, 150 chains. Longest chain 38 peptides. Score 0.472 Taking the results from Round 3 Chains 151, Residues 1323, Estimated correctness of the model 9.4 % 17 chains (305 residues) have been docked in sequence ------------------------------------------------------ 90855 reflections ( 99.15 % complete ) and 6562 restraints for refining 16998 atoms. Observations/parameters ratio is 1.34 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2289 (Rfree = 0.000) for 16998 atoms. Found 152 (152 requested) and removed 91 (76 requested) atoms. Cycle 37: After refmac, R = 0.2139 (Rfree = 0.000) for 17059 atoms. Found 93 (153 requested) and removed 82 (76 requested) atoms. Cycle 38: After refmac, R = 0.2073 (Rfree = 0.000) for 17070 atoms. Found 46 (153 requested) and removed 78 (76 requested) atoms. Cycle 39: After refmac, R = 0.2039 (Rfree = 0.000) for 17038 atoms. Found 25 (152 requested) and removed 76 (76 requested) atoms. Cycle 40: After refmac, R = 0.2024 (Rfree = 0.000) for 16987 atoms. Found 33 (152 requested) and removed 78 (76 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.03 1.83 Search for helices and strands: 0 residues in 0 chains, 17421 seeds are put forward NCS extension: 29 residues added (10 deleted due to clashes), 17450 seeds are put forward Round 1: 1393 peptides, 165 chains. Longest chain 30 peptides. Score 0.438 Round 2: 1492 peptides, 156 chains. Longest chain 41 peptides. Score 0.479 Round 3: 1459 peptides, 159 chains. Longest chain 38 peptides. Score 0.465 Round 4: 1476 peptides, 163 chains. Longest chain 41 peptides. Score 0.465 Round 5: 1452 peptides, 155 chains. Longest chain 34 peptides. Score 0.469 Taking the results from Round 2 Chains 168, Residues 1336, Estimated correctness of the model 4.4 % 18 chains (304 residues) have been docked in sequence ------------------------------------------------------ 90855 reflections ( 99.15 % complete ) and 6576 restraints for refining 17006 atoms. Observations/parameters ratio is 1.34 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2278 (Rfree = 0.000) for 17006 atoms. Found 152 (152 requested) and removed 90 (76 requested) atoms. Cycle 42: After refmac, R = 0.2146 (Rfree = 0.000) for 17068 atoms. Found 74 (153 requested) and removed 82 (76 requested) atoms. Cycle 43: After refmac, R = 0.2078 (Rfree = 0.000) for 17060 atoms. Found 42 (153 requested) and removed 79 (76 requested) atoms. Cycle 44: After refmac, R = 0.2057 (Rfree = 0.000) for 17023 atoms. Found 45 (152 requested) and removed 82 (76 requested) atoms. Cycle 45: After refmac, R = 0.2035 (Rfree = 0.000) for 16986 atoms. Found 37 (152 requested) and removed 77 (76 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.01 1.82 Search for helices and strands: 0 residues in 0 chains, 17412 seeds are put forward NCS extension: 27 residues added (11 deleted due to clashes), 17439 seeds are put forward Round 1: 1372 peptides, 157 chains. Longest chain 29 peptides. Score 0.443 Round 2: 1438 peptides, 151 chains. Longest chain 51 peptides. Score 0.471 Round 3: 1470 peptides, 147 chains. Longest chain 51 peptides. Score 0.485 Round 4: 1483 peptides, 153 chains. Longest chain 41 peptides. Score 0.480 Round 5: 1457 peptides, 143 chains. Longest chain 38 peptides. Score 0.487 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 157, Residues 1314, Estimated correctness of the model 7.1 % 17 chains (318 residues) have been docked in sequence Sequence coverage is 24 % Consider running further cycles of model building using 2aam-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 85 B and 98 B 153 chains (1311 residues) following loop building 16 chains (330 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 90855 reflections ( 99.15 % complete ) and 6391 restraints for refining 16870 atoms. Observations/parameters ratio is 1.35 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2373 (Rfree = 0.000) for 16870 atoms. Found 0 (151 requested) and removed 40 (75 requested) atoms. Cycle 47: After refmac, R = 0.2248 (Rfree = 0.000) for 16830 atoms. Found 0 (151 requested) and removed 16 (75 requested) atoms. Cycle 48: After refmac, R = 0.2202 (Rfree = 0.000) for 16814 atoms. Found 0 (150 requested) and removed 23 (75 requested) atoms. Cycle 49: After refmac, R = 0.2181 (Rfree = 0.000) for 16791 atoms. Found 0 (150 requested) and removed 11 (75 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 11:46:21 GMT 2018 Job finished. TimeTaking 229.86 Used memory is bytes: 15443768