Sun 23 Dec 23:43:13 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 1zko-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1zko-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1zko-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1zko-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/1zko-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1zko-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 23:43:17 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/1zko-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1zko-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 165 and 0 Target number of residues in the AU: 165 Target solvent content: 0.6342 Checking the provided sequence file Detected sequence length: 136 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 272 Adjusted target solvent content: 0.40 Input MTZ file: 1zko-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: 54.005 65.321 69.197 90.000 90.000 90.000 Input sequence file: 1zko-4.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 2176 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: 47.500 4.001 Wilson plot Bfac: 68.38 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 2121 reflections ( 93.19 % complete ) and 0 restraints for refining 2396 atoms. Observations/parameters ratio is 0.22 ------------------------------------------------------ Starting model: R = 0.3660 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3751 (Rfree = 0.000) for 2396 atoms. Found 11 (11 requested) and removed 31 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.58 4.10 Search for helices and strands: 0 residues in 0 chains, 2407 seeds are put forward NCS extension: 0 residues added, 2407 seeds are put forward Round 1: 29 peptides, 7 chains. Longest chain 5 peptides. Score 0.178 Round 2: 43 peptides, 10 chains. Longest chain 5 peptides. Score 0.196 Round 3: 52 peptides, 11 chains. Longest chain 8 peptides. Score 0.239 Round 4: 56 peptides, 12 chains. Longest chain 7 peptides. Score 0.237 Round 5: 71 peptides, 14 chains. Longest chain 8 peptides. Score 0.289 Taking the results from Round 5 Chains 14, Residues 57, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2121 reflections ( 93.19 % complete ) and 4381 restraints for refining 1870 atoms. 4167 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3133 (Rfree = 0.000) for 1870 atoms. Found 8 (8 requested) and removed 169 (4 requested) atoms. Cycle 2: After refmac, R = 0.2776 (Rfree = 0.000) for 1696 atoms. Found 8 (8 requested) and removed 19 (4 requested) atoms. Cycle 3: After refmac, R = 0.2932 (Rfree = 0.000) for 1672 atoms. Found 8 (8 requested) and removed 15 (4 requested) atoms. Failed to save intermediate PDB Cycle 4: After refmac, R = 0.2482 (Rfree = 0.000) for 1649 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. Cycle 5: After refmac, R = 0.2241 (Rfree = 0.000) for 1641 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.58 4.10 Search for helices and strands: 0 residues in 0 chains, 1670 seeds are put forward NCS extension: 0 residues added, 1670 seeds are put forward Round 1: 65 peptides, 15 chains. Longest chain 6 peptides. Score 0.209 Round 2: 81 peptides, 17 chains. Longest chain 7 peptides. Score 0.269 Round 3: 91 peptides, 18 chains. Longest chain 13 peptides. Score 0.312 Round 4: 94 peptides, 19 chains. Longest chain 10 peptides. Score 0.303 Round 5: 95 peptides, 18 chains. Longest chain 10 peptides. Score 0.340 Taking the results from Round 5 Chains 18, Residues 77, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2121 reflections ( 93.19 % complete ) and 3828 restraints for refining 1653 atoms. 3538 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2678 (Rfree = 0.000) for 1653 atoms. Found 7 (7 requested) and removed 34 (3 requested) atoms. Cycle 7: After refmac, R = 0.2143 (Rfree = 0.000) for 1615 atoms. Found 4 (7 requested) and removed 9 (3 requested) atoms. Cycle 8: After refmac, R = 0.1947 (Rfree = 0.000) for 1607 atoms. Found 2 (7 requested) and removed 7 (3 requested) atoms. Cycle 9: After refmac, R = 0.2093 (Rfree = 0.000) for 1597 atoms. Found 5 (7 requested) and removed 9 (3 requested) atoms. Cycle 10: After refmac, R = 0.1892 (Rfree = 0.000) for 1593 atoms. Found 2 (7 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.52 4.03 Search for helices and strands: 0 residues in 0 chains, 1628 seeds are put forward NCS extension: 0 residues added, 1628 seeds are put forward Round 1: 104 peptides, 21 chains. Longest chain 9 peptides. Score 0.315 Round 2: 97 peptides, 18 chains. Longest chain 9 peptides. Score 0.354 Round 3: 95 peptides, 18 chains. Longest chain 11 peptides. Score 0.340 Round 4: 100 peptides, 20 chains. Longest chain 11 peptides. Score 0.316 Round 5: 90 peptides, 17 chains. Longest chain 10 peptides. Score 0.335 Taking the results from Round 2 Chains 18, Residues 79, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2121 reflections ( 93.19 % complete ) and 3970 restraints for refining 1721 atoms. 3672 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2264 (Rfree = 0.000) for 1721 atoms. Found 7 (8 requested) and removed 31 (4 requested) atoms. Cycle 12: After refmac, R = 0.1826 (Rfree = 0.000) for 1690 atoms. Found 7 (8 requested) and removed 20 (4 requested) atoms. Cycle 13: After refmac, R = 0.1821 (Rfree = 0.000) for 1670 atoms. Found 3 (7 requested) and removed 6 (3 requested) atoms. Cycle 14: After refmac, R = 0.1699 (Rfree = 0.000) for 1665 atoms. Found 5 (7 requested) and removed 5 (3 requested) atoms. Cycle 15: After refmac, R = 0.1702 (Rfree = 0.000) for 1663 atoms. Found 5 (7 requested) and removed 7 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.54 4.05 Search for helices and strands: 0 residues in 0 chains, 1695 seeds are put forward NCS extension: 0 residues added, 1695 seeds are put forward Round 1: 85 peptides, 18 chains. Longest chain 7 peptides. Score 0.268 Round 2: 87 peptides, 15 chains. Longest chain 10 peptides. Score 0.374 Round 3: 79 peptides, 16 chains. Longest chain 7 peptides. Score 0.286 Round 4: 91 peptides, 17 chains. Longest chain 7 peptides. Score 0.342 Round 5: 96 peptides, 17 chains. Longest chain 9 peptides. Score 0.376 Taking the results from Round 5 Chains 17, Residues 79, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2121 reflections ( 93.19 % complete ) and 4227 restraints for refining 1791 atoms. 3928 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2431 (Rfree = 0.000) for 1791 atoms. Found 6 (8 requested) and removed 69 (4 requested) atoms. Cycle 17: After refmac, R = 0.2554 (Rfree = 0.000) for 1711 atoms. Found 8 (8 requested) and removed 35 (4 requested) atoms. Cycle 18: After refmac, R = 0.2065 (Rfree = 0.000) for 1671 atoms. Found 7 (7 requested) and removed 14 (3 requested) atoms. Cycle 19: After refmac, R = 0.2443 (Rfree = 0.000) for 1649 atoms. Found 7 (7 requested) and removed 15 (3 requested) atoms. Cycle 20: After refmac, R = 0.2668 (Rfree = 0.000) for 1624 atoms. Found 7 (7 requested) and removed 13 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.57 4.09 Search for helices and strands: 0 residues in 0 chains, 1658 seeds are put forward NCS extension: 0 residues added, 1658 seeds are put forward Round 1: 49 peptides, 10 chains. Longest chain 7 peptides. Score 0.250 Round 2: 80 peptides, 17 chains. Longest chain 10 peptides. Score 0.262 Round 3: 74 peptides, 15 chains. Longest chain 9 peptides. Score 0.280 Round 4: 73 peptides, 14 chains. Longest chain 13 peptides. Score 0.305 Round 5: 72 peptides, 13 chains. Longest chain 9 peptides. Score 0.329 Taking the results from Round 5 Chains 13, Residues 59, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2121 reflections ( 93.19 % complete ) and 3459 restraints for refining 1548 atoms. 3236 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3284 (Rfree = 0.000) for 1548 atoms. Found 7 (7 requested) and removed 26 (3 requested) atoms. Cycle 22: After refmac, R = 0.3195 (Rfree = 0.000) for 1509 atoms. Found 7 (7 requested) and removed 15 (3 requested) atoms. Cycle 23: After refmac, R = 0.2890 (Rfree = 0.000) for 1484 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. Cycle 24: After refmac, R = 0.3597 (Rfree = 0.000) for 1475 atoms. Found 7 (7 requested) and removed 11 (3 requested) atoms. Cycle 25: After refmac, R = 0.3265 (Rfree = 0.000) for 1461 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.50 4.01 Search for helices and strands: 0 residues in 0 chains, 1494 seeds are put forward NCS extension: 0 residues added, 1494 seeds are put forward Round 1: 54 peptides, 12 chains. Longest chain 9 peptides. Score 0.220 Round 2: 88 peptides, 19 chains. Longest chain 8 peptides. Score 0.260 Round 3: 94 peptides, 19 chains. Longest chain 11 peptides. Score 0.303 Round 4: 86 peptides, 16 chains. Longest chain 12 peptides. Score 0.337 Round 5: 86 peptides, 16 chains. Longest chain 11 peptides. Score 0.337 Taking the results from Round 5 Chains 16, Residues 70, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2121 reflections ( 93.19 % complete ) and 3134 restraints for refining 1438 atoms. 2870 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2814 (Rfree = 0.000) for 1438 atoms. Found 6 (6 requested) and removed 20 (3 requested) atoms. Cycle 27: After refmac, R = 0.2690 (Rfree = 0.000) for 1416 atoms. Found 6 (6 requested) and removed 10 (3 requested) atoms. Cycle 28: After refmac, R = 0.2170 (Rfree = 0.000) for 1404 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. Cycle 29: After refmac, R = 0.2145 (Rfree = 0.000) for 1401 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. Cycle 30: After refmac, R = 0.2474 (Rfree = 0.000) for 1398 atoms. Found 6 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.55 4.06 Search for helices and strands: 0 residues in 0 chains, 1446 seeds are put forward NCS extension: 0 residues added, 1446 seeds are put forward Round 1: 61 peptides, 14 chains. Longest chain 5 peptides. Score 0.210 Round 2: 64 peptides, 13 chains. Longest chain 7 peptides. Score 0.268 Round 3: 67 peptides, 13 chains. Longest chain 7 peptides. Score 0.292 Round 4: 68 peptides, 13 chains. Longest chain 8 peptides. Score 0.299 Round 5: 64 peptides, 11 chains. Longest chain 8 peptides. Score 0.335 Taking the results from Round 5 Chains 11, Residues 53, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2121 reflections ( 93.19 % complete ) and 3126 restraints for refining 1424 atoms. 2925 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3010 (Rfree = 0.000) for 1424 atoms. Found 6 (6 requested) and removed 37 (3 requested) atoms. Cycle 32: After refmac, R = 0.2692 (Rfree = 0.000) for 1383 atoms. Found 6 (6 requested) and removed 21 (3 requested) atoms. Cycle 33: After refmac, R = 0.2711 (Rfree = 0.000) for 1358 atoms. Found 6 (6 requested) and removed 11 (3 requested) atoms. Cycle 34: After refmac, R = 0.2689 (Rfree = 0.000) for 1347 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. Cycle 35: After refmac, R = 0.2283 (Rfree = 0.000) for 1340 atoms. Found 6 (6 requested) and removed 12 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.60 4.12 Search for helices and strands: 0 residues in 0 chains, 1373 seeds are put forward NCS extension: 0 residues added, 1373 seeds are put forward Round 1: 42 peptides, 10 chains. Longest chain 5 peptides. Score 0.186 Round 2: 64 peptides, 13 chains. Longest chain 7 peptides. Score 0.268 Round 3: 66 peptides, 14 chains. Longest chain 8 peptides. Score 0.251 Round 4: 70 peptides, 13 chains. Longest chain 9 peptides. Score 0.314 Round 5: 74 peptides, 14 chains. Longest chain 10 peptides. Score 0.312 Taking the results from Round 4 Chains 13, Residues 57, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2121 reflections ( 93.19 % complete ) and 2614 restraints for refining 1246 atoms. 2399 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2877 (Rfree = 0.000) for 1246 atoms. Found 5 (5 requested) and removed 15 (2 requested) atoms. Cycle 37: After refmac, R = 0.2804 (Rfree = 0.000) for 1228 atoms. Found 5 (5 requested) and removed 18 (2 requested) atoms. Cycle 38: After refmac, R = 0.2672 (Rfree = 0.000) for 1211 atoms. Found 5 (5 requested) and removed 6 (2 requested) atoms. Cycle 39: After refmac, R = 0.2482 (Rfree = 0.000) for 1204 atoms. Found 5 (5 requested) and removed 4 (2 requested) atoms. Cycle 40: After refmac, R = 0.2524 (Rfree = 0.000) for 1204 atoms. Found 5 (5 requested) and removed 8 (2 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.76 4.30 Search for helices and strands: 0 residues in 0 chains, 1245 seeds are put forward NCS extension: 0 residues added, 1245 seeds are put forward Round 1: 54 peptides, 12 chains. Longest chain 7 peptides. Score 0.220 Round 2: 65 peptides, 13 chains. Longest chain 6 peptides. Score 0.276 Round 3: 67 peptides, 13 chains. Longest chain 10 peptides. Score 0.292 Round 4: 69 peptides, 13 chains. Longest chain 10 peptides. Score 0.307 Round 5: 70 peptides, 14 chains. Longest chain 8 peptides. Score 0.282 Taking the results from Round 4 Chains 13, Residues 56, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2121 reflections ( 93.19 % complete ) and 2704 restraints for refining 1286 atoms. 2493 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3057 (Rfree = 0.000) for 1286 atoms. Found 6 (6 requested) and removed 13 (3 requested) atoms. Cycle 42: After refmac, R = 0.2949 (Rfree = 0.000) for 1273 atoms. Found 6 (6 requested) and removed 4 (3 requested) atoms. Cycle 43: After refmac, R = 0.2958 (Rfree = 0.000) for 1272 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. Cycle 44: After refmac, R = 0.2837 (Rfree = 0.000) for 1269 atoms. Found 6 (6 requested) and removed 9 (3 requested) atoms. Cycle 45: After refmac, R = 0.2544 (Rfree = 0.000) for 1266 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.71 4.25 Search for helices and strands: 0 residues in 0 chains, 1293 seeds are put forward NCS extension: 0 residues added, 1293 seeds are put forward Round 1: 57 peptides, 13 chains. Longest chain 7 peptides. Score 0.211 Round 2: 65 peptides, 14 chains. Longest chain 6 peptides. Score 0.242 Round 3: 67 peptides, 13 chains. Longest chain 7 peptides. Score 0.292 Round 4: 67 peptides, 13 chains. Longest chain 7 peptides. Score 0.292 Round 5: 65 peptides, 13 chains. Longest chain 7 peptides. Score 0.276 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 13, Residues 54, 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 1zko-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2121 reflections ( 93.19 % complete ) and 2991 restraints for refining 1347 atoms. 2788 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3334 (Rfree = 0.000) for 1347 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.3129 (Rfree = 0.000) for 1334 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.3224 (Rfree = 0.000) for 1324 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.2826 (Rfree = 0.000) for 1316 atoms. TimeTaking 21.83