Mon 24 Dec 00:35:14 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 2pg4-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2pg4-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2pg4-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pg4-3.2-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/2pg4-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pg4-3.2-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 ============================================================ Mon 24 Dec 00:35:18 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/2pg4-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pg4-3.2-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 149 and 0 Target number of residues in the AU: 149 Target solvent content: 0.6364 Checking the provided sequence file Detected sequence length: 95 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 190 Adjusted target solvent content: 0.54 Input MTZ file: 2pg4-3.2-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: 90 Cell parameters: 109.840 109.840 36.760 90.000 90.000 90.000 Input sequence file: 2pg4-3.2-parrot-mrncs.fasta_lf Building free atoms model in initial map for 1520 target number of atoms Had to go as low as 0.70 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: 77.669 3.201 Wilson plot Bfac: 68.80 4027 reflections ( 99.65 % complete ) and 0 restraints for refining 1688 atoms. Observations/parameters ratio is 0.60 ------------------------------------------------------ Starting model: R = 0.3738 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3342 (Rfree = 0.000) for 1688 atoms. Found 14 (15 requested) and removed 16 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.25 3.08 Search for helices and strands: 0 residues in 0 chains, 1721 seeds are put forward NCS extension: 0 residues added, 1721 seeds are put forward Round 1: 77 peptides, 13 chains. Longest chain 12 peptides. Score 0.380 Round 2: 93 peptides, 14 chains. Longest chain 14 peptides. Score 0.463 Round 3: 119 peptides, 19 chains. Longest chain 14 peptides. Score 0.490 Round 4: 112 peptides, 12 chains. Longest chain 23 peptides. Score 0.630 Round 5: 107 peptides, 13 chains. Longest chain 17 peptides. Score 0.578 Taking the results from Round 4 Chains 12, Residues 100, Estimated correctness of the model 48.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4027 reflections ( 99.65 % complete ) and 3108 restraints for refining 1387 atoms. 2720 conditional restraints added. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3112 (Rfree = 0.000) for 1387 atoms. Found 5 (12 requested) and removed 12 (6 requested) atoms. Cycle 2: After refmac, R = 0.3269 (Rfree = 0.000) for 1356 atoms. Found 8 (12 requested) and removed 12 (6 requested) atoms. Cycle 3: After refmac, R = 0.3015 (Rfree = 0.000) for 1348 atoms. Found 2 (12 requested) and removed 7 (6 requested) atoms. Cycle 4: After refmac, R = 0.3121 (Rfree = 0.000) for 1339 atoms. Found 8 (12 requested) and removed 9 (6 requested) atoms. Cycle 5: After refmac, R = 0.3151 (Rfree = 0.000) for 1330 atoms. Found 4 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.27 3.10 Search for helices and strands: 0 residues in 0 chains, 1390 seeds are put forward NCS extension: 35 residues added (2 deleted due to clashes), 1425 seeds are put forward Round 1: 88 peptides, 15 chains. Longest chain 11 peptides. Score 0.397 Round 2: 109 peptides, 15 chains. Longest chain 20 peptides. Score 0.537 Round 3: 120 peptides, 15 chains. Longest chain 15 peptides. Score 0.600 Round 4: 122 peptides, 13 chains. Longest chain 22 peptides. Score 0.656 Round 5: 121 peptides, 14 chains. Longest chain 17 peptides. Score 0.629 Taking the results from Round 4 Chains 13, Residues 109, Estimated correctness of the model 55.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4027 reflections ( 99.65 % complete ) and 2903 restraints for refining 1338 atoms. 2480 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3073 (Rfree = 0.000) for 1338 atoms. Found 6 (11 requested) and removed 12 (5 requested) atoms. Cycle 7: After refmac, R = 0.2906 (Rfree = 0.000) for 1326 atoms. Found 11 (11 requested) and removed 6 (5 requested) atoms. Cycle 8: After refmac, R = 0.3375 (Rfree = 0.000) for 1324 atoms. Found 11 (11 requested) and removed 6 (5 requested) atoms. Cycle 9: After refmac, R = 0.2765 (Rfree = 0.000) for 1324 atoms. Found 4 (11 requested) and removed 5 (5 requested) atoms. Cycle 10: After refmac, R = 0.2682 (Rfree = 0.000) for 1321 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.24 3.07 Search for helices and strands: 0 residues in 0 chains, 1377 seeds are put forward NCS extension: 46 residues added (3 deleted due to clashes), 1423 seeds are put forward Round 1: 111 peptides, 16 chains. Longest chain 18 peptides. Score 0.522 Round 2: 114 peptides, 13 chains. Longest chain 23 peptides. Score 0.616 Round 3: 123 peptides, 13 chains. Longest chain 22 peptides. Score 0.661 Round 4: 126 peptides, 13 chains. Longest chain 38 peptides. Score 0.675 Round 5: 122 peptides, 12 chains. Longest chain 28 peptides. Score 0.678 Taking the results from Round 5 Chains 12, Residues 110, Estimated correctness of the model 60.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4027 reflections ( 99.65 % complete ) and 2907 restraints for refining 1361 atoms. 2479 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3077 (Rfree = 0.000) for 1361 atoms. Found 11 (12 requested) and removed 13 (6 requested) atoms. Cycle 12: After refmac, R = 0.2960 (Rfree = 0.000) for 1351 atoms. Found 1 (12 requested) and removed 9 (6 requested) atoms. Cycle 13: After refmac, R = 0.2695 (Rfree = 0.000) for 1342 atoms. Found 3 (12 requested) and removed 6 (6 requested) atoms. Cycle 14: After refmac, R = 0.2647 (Rfree = 0.000) for 1339 atoms. Found 1 (11 requested) and removed 5 (5 requested) atoms. Cycle 15: After refmac, R = 0.2643 (Rfree = 0.000) for 1332 atoms. Found 2 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.31 3.14 Search for helices and strands: 0 residues in 0 chains, 1390 seeds are put forward NCS extension: 41 residues added (6 deleted due to clashes), 1431 seeds are put forward Round 1: 111 peptides, 14 chains. Longest chain 20 peptides. Score 0.575 Round 2: 115 peptides, 12 chains. Longest chain 20 peptides. Score 0.645 Round 3: 116 peptides, 12 chains. Longest chain 22 peptides. Score 0.650 Round 4: 123 peptides, 13 chains. Longest chain 23 peptides. Score 0.661 Round 5: 120 peptides, 11 chains. Longest chain 25 peptides. Score 0.691 Taking the results from Round 5 Chains 11, Residues 109, Estimated correctness of the model 63.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4027 reflections ( 99.65 % complete ) and 3004 restraints for refining 1387 atoms. 2579 conditional restraints added. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3105 (Rfree = 0.000) for 1387 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. Cycle 17: After refmac, R = 0.3024 (Rfree = 0.000) for 1385 atoms. Found 6 (12 requested) and removed 9 (6 requested) atoms. Cycle 18: After refmac, R = 0.2803 (Rfree = 0.000) for 1376 atoms. Found 1 (12 requested) and removed 8 (6 requested) atoms. Cycle 19: After refmac, R = 0.2732 (Rfree = 0.000) for 1365 atoms. Found 0 (12 requested) and removed 7 (6 requested) atoms. Cycle 20: After refmac, R = 0.2888 (Rfree = 0.000) for 1356 atoms. Found 0 (12 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.27 3.10 Search for helices and strands: 0 residues in 0 chains, 1417 seeds are put forward NCS extension: 35 residues added (4 deleted due to clashes), 1452 seeds are put forward Round 1: 106 peptides, 13 chains. Longest chain 25 peptides. Score 0.572 Round 2: 119 peptides, 14 chains. Longest chain 23 peptides. Score 0.618 Round 3: 120 peptides, 12 chains. Longest chain 27 peptides. Score 0.669 Round 4: 124 peptides, 12 chains. Longest chain 25 peptides. Score 0.687 Round 5: 133 peptides, 14 chains. Longest chain 22 peptides. Score 0.686 Taking the results from Round 4 Chains 12, Residues 112, Estimated correctness of the model 62.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4027 reflections ( 99.65 % complete ) and 2923 restraints for refining 1372 atoms. 2487 conditional restraints added. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2921 (Rfree = 0.000) for 1372 atoms. Found 4 (12 requested) and removed 7 (6 requested) atoms. Cycle 22: After refmac, R = 0.2846 (Rfree = 0.000) for 1365 atoms. Found 1 (12 requested) and removed 7 (6 requested) atoms. Cycle 23: After refmac, R = 0.3244 (Rfree = 0.000) for 1357 atoms. Found 8 (12 requested) and removed 9 (6 requested) atoms. Cycle 24: After refmac, R = 0.2901 (Rfree = 0.000) for 1348 atoms. Found 3 (12 requested) and removed 8 (6 requested) atoms. Cycle 25: After refmac, R = 0.2904 (Rfree = 0.000) for 1338 atoms. Found 1 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.28 3.11 Search for helices and strands: 0 residues in 0 chains, 1399 seeds are put forward NCS extension: 29 residues added (3 deleted due to clashes), 1428 seeds are put forward Round 1: 94 peptides, 12 chains. Longest chain 24 peptides. Score 0.528 Round 2: 111 peptides, 14 chains. Longest chain 23 peptides. Score 0.575 Round 3: 114 peptides, 13 chains. Longest chain 24 peptides. Score 0.616 Round 4: 116 peptides, 12 chains. Longest chain 24 peptides. Score 0.650 Round 5: 105 peptides, 14 chains. Longest chain 19 peptides. Score 0.540 Taking the results from Round 4 Chains 14, Residues 104, Estimated correctness of the model 53.8 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 4027 reflections ( 99.65 % complete ) and 2847 restraints for refining 1362 atoms. 2409 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2907 (Rfree = 0.000) for 1362 atoms. Found 5 (12 requested) and removed 10 (6 requested) atoms. Cycle 27: After refmac, R = 0.3343 (Rfree = 0.000) for 1355 atoms. Found 6 (12 requested) and removed 11 (6 requested) atoms. Cycle 28: After refmac, R = 0.2958 (Rfree = 0.000) for 1346 atoms. Found 2 (12 requested) and removed 7 (6 requested) atoms. Cycle 29: After refmac, R = 0.2845 (Rfree = 0.000) for 1337 atoms. Found 0 (12 requested) and removed 7 (6 requested) atoms. Cycle 30: After refmac, R = 0.2722 (Rfree = 0.000) for 1323 atoms. Found 2 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.29 3.12 Search for helices and strands: 0 residues in 0 chains, 1384 seeds are put forward NCS extension: 25 residues added (1 deleted due to clashes), 1409 seeds are put forward Round 1: 103 peptides, 15 chains. Longest chain 24 peptides. Score 0.499 Round 2: 104 peptides, 15 chains. Longest chain 18 peptides. Score 0.506 Round 3: 106 peptides, 13 chains. Longest chain 19 peptides. Score 0.572 Round 4: 110 peptides, 15 chains. Longest chain 20 peptides. Score 0.543 Round 5: 109 peptides, 13 chains. Longest chain 21 peptides. Score 0.589 Taking the results from Round 5 Chains 13, Residues 96, Estimated correctness of the model 38.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4027 reflections ( 99.65 % complete ) and 3010 restraints for refining 1370 atoms. 2639 conditional restraints added. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2907 (Rfree = 0.000) for 1370 atoms. Found 5 (12 requested) and removed 37 (6 requested) atoms. Cycle 32: After refmac, R = 0.3073 (Rfree = 0.000) for 1336 atoms. Found 6 (11 requested) and removed 10 (5 requested) atoms. Cycle 33: After refmac, R = 0.2735 (Rfree = 0.000) for 1329 atoms. Found 3 (11 requested) and removed 7 (5 requested) atoms. Cycle 34: After refmac, R = 0.2754 (Rfree = 0.000) for 1323 atoms. Found 1 (11 requested) and removed 7 (5 requested) atoms. Cycle 35: After refmac, R = 0.2734 (Rfree = 0.000) for 1316 atoms. Found 8 (11 requested) and removed 64 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.25 3.08 Search for helices and strands: 0 residues in 0 chains, 1303 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 1327 seeds are put forward Round 1: 58 peptides, 13 chains. Longest chain 6 peptides. Score 0.223 Round 2: 64 peptides, 13 chains. Longest chain 6 peptides. Score 0.275 Round 3: 53 peptides, 10 chains. Longest chain 7 peptides. Score 0.291 Round 4: 55 peptides, 10 chains. Longest chain 8 peptides. Score 0.309 Round 5: 59 peptides, 11 chains. Longest chain 8 peptides. Score 0.305 Taking the results from Round 4 Chains 10, Residues 45, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4027 reflections ( 99.65 % complete ) and 3278 restraints for refining 1387 atoms. 3108 conditional restraints added. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3821 (Rfree = 0.000) for 1387 atoms. Found 11 (12 requested) and removed 26 (6 requested) atoms. Cycle 37: After refmac, R = 0.3441 (Rfree = 0.000) for 1372 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 38: After refmac, R = 0.3054 (Rfree = 0.000) for 1371 atoms. Found 7 (12 requested) and removed 6 (6 requested) atoms. Cycle 39: After refmac, R = 0.2897 (Rfree = 0.000) for 1365 atoms. Found 5 (12 requested) and removed 8 (6 requested) atoms. Cycle 40: After refmac, R = 0.2799 (Rfree = 0.000) for 1355 atoms. Found 4 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.25 3.08 Search for helices and strands: 0 residues in 0 chains, 1407 seeds are put forward NCS extension: 0 residues added, 1407 seeds are put forward Round 1: 46 peptides, 10 chains. Longest chain 6 peptides. Score 0.227 Round 2: 62 peptides, 11 chains. Longest chain 12 peptides. Score 0.330 Round 3: 63 peptides, 11 chains. Longest chain 10 peptides. Score 0.339 Round 4: 61 peptides, 10 chains. Longest chain 11 peptides. Score 0.358 Round 5: 66 peptides, 10 chains. Longest chain 11 peptides. Score 0.397 Taking the results from Round 5 Chains 10, Residues 56, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4027 reflections ( 99.65 % complete ) and 3201 restraints for refining 1380 atoms. 2987 conditional restraints added. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2993 (Rfree = 0.000) for 1380 atoms. Found 9 (12 requested) and removed 7 (6 requested) atoms. Cycle 42: After refmac, R = 0.2821 (Rfree = 0.000) for 1381 atoms. Found 6 (12 requested) and removed 8 (6 requested) atoms. Cycle 43: After refmac, R = 0.2709 (Rfree = 0.000) for 1375 atoms. Found 2 (12 requested) and removed 6 (6 requested) atoms. Cycle 44: After refmac, R = 0.3048 (Rfree = 0.000) for 1369 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. Cycle 45: After refmac, R = 0.2847 (Rfree = 0.000) for 1372 atoms. Found 7 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.22 3.05 Search for helices and strands: 0 residues in 0 chains, 1412 seeds are put forward NCS extension: 0 residues added, 1412 seeds are put forward Round 1: 59 peptides, 10 chains. Longest chain 9 peptides. Score 0.342 Round 2: 74 peptides, 14 chains. Longest chain 9 peptides. Score 0.323 Round 3: 71 peptides, 11 chains. Longest chain 14 peptides. Score 0.401 Round 4: 73 peptides, 11 chains. Longest chain 14 peptides. Score 0.416 Round 5: 73 peptides, 12 chains. Longest chain 14 peptides. Score 0.382 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 11, Residues 62, 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 2pg4-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. Failed to save intermediate PDB 4027 reflections ( 99.65 % complete ) and 3044 restraints for refining 1356 atoms. 2807 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2635 (Rfree = 0.000) for 1356 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.2728 (Rfree = 0.000) for 1347 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.2784 (Rfree = 0.000) for 1338 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.2550 (Rfree = 0.000) for 1328 atoms. TimeTaking 24.85