Sun 23 Dec 23:52:01 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 2fno-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2fno-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2fno-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fno-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/2fno-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fno-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 23:52:06 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/2fno-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fno-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 366 and 0 Target number of residues in the AU: 366 Target solvent content: 0.6627 Checking the provided sequence file Detected sequence length: 248 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 496 Adjusted target solvent content: 0.54 Input MTZ file: 2fno-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: 5 Cell parameters: 110.204 50.261 117.660 90.000 115.716 90.000 Input sequence file: 2fno-4.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 3968 target number of atoms Had to go as low as 0.80 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: 106.006 4.000 Wilson plot Bfac: 86.43 5042 reflections ( 98.94 % complete ) and 0 restraints for refining 4370 atoms. Observations/parameters ratio is 0.29 ------------------------------------------------------ Starting model: R = 0.3503 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3536 (Rfree = 0.000) for 4370 atoms. Found 20 (20 requested) and removed 144 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.71 3.52 Search for helices and strands: 0 residues in 0 chains, 4350 seeds are put forward NCS extension: 0 residues added, 4350 seeds are put forward Round 1: 178 peptides, 38 chains. Longest chain 11 peptides. Score 0.254 Round 2: 203 peptides, 37 chains. Longest chain 10 peptides. Score 0.344 Round 3: 219 peptides, 39 chains. Longest chain 12 peptides. Score 0.366 Round 4: 245 peptides, 39 chains. Longest chain 12 peptides. Score 0.437 Round 5: 252 peptides, 41 chains. Longest chain 12 peptides. Score 0.433 Taking the results from Round 4 Chains 39, Residues 206, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 5042 reflections ( 98.94 % complete ) and 8480 restraints for refining 3577 atoms. 7685 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2706 (Rfree = 0.000) for 3577 atoms. Found 17 (17 requested) and removed 36 (8 requested) atoms. Cycle 2: After refmac, R = 0.2555 (Rfree = 0.000) for 3528 atoms. Found 16 (16 requested) and removed 26 (8 requested) atoms. Cycle 3: After refmac, R = 0.2442 (Rfree = 0.000) for 3496 atoms. Found 16 (16 requested) and removed 24 (8 requested) atoms. Cycle 4: After refmac, R = 0.2074 (Rfree = 0.000) for 3479 atoms. Found 16 (16 requested) and removed 17 (8 requested) atoms. Cycle 5: After refmac, R = 0.1937 (Rfree = 0.000) for 3468 atoms. Found 16 (16 requested) and removed 16 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.80 3.60 Search for helices and strands: 0 residues in 0 chains, 3599 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 3615 seeds are put forward Round 1: 211 peptides, 41 chains. Longest chain 9 peptides. Score 0.317 Round 2: 220 peptides, 38 chains. Longest chain 16 peptides. Score 0.381 Round 3: 219 peptides, 37 chains. Longest chain 12 peptides. Score 0.390 Round 4: 229 peptides, 34 chains. Longest chain 19 peptides. Score 0.453 Round 5: 232 peptides, 36 chains. Longest chain 18 peptides. Score 0.438 Taking the results from Round 4 Chains 34, Residues 195, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 5042 reflections ( 98.94 % complete ) and 8586 restraints for refining 3580 atoms. 7826 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2590 (Rfree = 0.000) for 3580 atoms. Found 17 (17 requested) and removed 35 (8 requested) atoms. Cycle 7: After refmac, R = 0.2418 (Rfree = 0.000) for 3536 atoms. Found 16 (16 requested) and removed 34 (8 requested) atoms. Cycle 8: After refmac, R = 0.2216 (Rfree = 0.000) for 3507 atoms. Found 16 (16 requested) and removed 21 (8 requested) atoms. Cycle 9: After refmac, R = 0.2155 (Rfree = 0.000) for 3486 atoms. Found 16 (16 requested) and removed 24 (8 requested) atoms. Cycle 10: After refmac, R = 0.2173 (Rfree = 0.000) for 3470 atoms. Found 16 (16 requested) and removed 45 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.87 3.67 Search for helices and strands: 0 residues in 0 chains, 3571 seeds are put forward NCS extension: 30 residues added (0 deleted due to clashes), 3601 seeds are put forward Round 1: 200 peptides, 38 chains. Longest chain 12 peptides. Score 0.323 Round 2: 224 peptides, 33 chains. Longest chain 18 peptides. Score 0.452 Round 3: 231 peptides, 34 chains. Longest chain 11 peptides. Score 0.458 Round 4: 221 peptides, 34 chains. Longest chain 21 peptides. Score 0.432 Round 5: 231 peptides, 36 chains. Longest chain 18 peptides. Score 0.435 Taking the results from Round 3 Chains 34, Residues 197, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5042 reflections ( 98.94 % complete ) and 8570 restraints for refining 3581 atoms. 7816 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2388 (Rfree = 0.000) for 3581 atoms. Found 17 (17 requested) and removed 29 (8 requested) atoms. Cycle 12: After refmac, R = 0.2387 (Rfree = 0.000) for 3554 atoms. Found 16 (16 requested) and removed 28 (8 requested) atoms. Cycle 13: After refmac, R = 0.2187 (Rfree = 0.000) for 3533 atoms. Found 16 (16 requested) and removed 19 (8 requested) atoms. Cycle 14: After refmac, R = 0.1834 (Rfree = 0.000) for 3518 atoms. Found 9 (16 requested) and removed 26 (8 requested) atoms. Cycle 15: After refmac, R = 0.1747 (Rfree = 0.000) for 3492 atoms. Found 1 (16 requested) and removed 14 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.81 3.61 Search for helices and strands: 0 residues in 0 chains, 3634 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 3647 seeds are put forward Round 1: 175 peptides, 34 chains. Longest chain 10 peptides. Score 0.298 Round 2: 195 peptides, 32 chains. Longest chain 20 peptides. Score 0.384 Round 3: 207 peptides, 33 chains. Longest chain 16 peptides. Score 0.406 Round 4: 206 peptides, 34 chains. Longest chain 10 peptides. Score 0.391 Round 5: 209 peptides, 31 chains. Longest chain 18 peptides. Score 0.436 Taking the results from Round 5 Chains 31, Residues 178, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5042 reflections ( 98.94 % complete ) and 8700 restraints for refining 3583 atoms. 8019 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2311 (Rfree = 0.000) for 3583 atoms. Found 17 (17 requested) and removed 32 (8 requested) atoms. Cycle 17: After refmac, R = 0.2256 (Rfree = 0.000) for 3548 atoms. Found 16 (16 requested) and removed 30 (8 requested) atoms. Cycle 18: After refmac, R = 0.2241 (Rfree = 0.000) for 3522 atoms. Found 16 (16 requested) and removed 18 (8 requested) atoms. Cycle 19: After refmac, R = 0.2158 (Rfree = 0.000) for 3514 atoms. Found 16 (16 requested) and removed 20 (8 requested) atoms. Cycle 20: After refmac, R = 0.2125 (Rfree = 0.000) for 3505 atoms. Found 16 (16 requested) and removed 15 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.85 3.65 Search for helices and strands: 0 residues in 0 chains, 3654 seeds are put forward NCS extension: 31 residues added (0 deleted due to clashes), 3685 seeds are put forward Round 1: 190 peptides, 37 chains. Longest chain 15 peptides. Score 0.305 Round 2: 197 peptides, 35 chains. Longest chain 11 peptides. Score 0.352 Round 3: 219 peptides, 34 chains. Longest chain 19 peptides. Score 0.427 Round 4: 216 peptides, 35 chains. Longest chain 12 peptides. Score 0.406 Round 5: 219 peptides, 35 chains. Longest chain 16 peptides. Score 0.415 Taking the results from Round 3 Chains 34, Residues 185, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5042 reflections ( 98.94 % complete ) and 8441 restraints for refining 3583 atoms. 7735 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2372 (Rfree = 0.000) for 3583 atoms. Found 17 (17 requested) and removed 41 (8 requested) atoms. Cycle 22: After refmac, R = 0.2267 (Rfree = 0.000) for 3542 atoms. Found 16 (16 requested) and removed 20 (8 requested) atoms. Cycle 23: After refmac, R = 0.2208 (Rfree = 0.000) for 3529 atoms. Found 16 (16 requested) and removed 24 (8 requested) atoms. Cycle 24: After refmac, R = 0.2030 (Rfree = 0.000) for 3515 atoms. Found 16 (16 requested) and removed 18 (8 requested) atoms. Cycle 25: After refmac, R = 0.1600 (Rfree = 0.000) for 3506 atoms. Found 10 (16 requested) and removed 16 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.84 3.64 Search for helices and strands: 0 residues in 0 chains, 3639 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 3652 seeds are put forward Round 1: 164 peptides, 32 chains. Longest chain 11 peptides. Score 0.291 Round 2: 200 peptides, 33 chains. Longest chain 10 peptides. Score 0.386 Round 3: 190 peptides, 27 chains. Longest chain 14 peptides. Score 0.433 Round 4: 192 peptides, 26 chains. Longest chain 15 peptides. Score 0.451 Round 5: 199 peptides, 29 chains. Longest chain 15 peptides. Score 0.433 Taking the results from Round 4 Chains 26, Residues 166, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 5042 reflections ( 98.94 % complete ) and 8568 restraints for refining 3583 atoms. 7918 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2429 (Rfree = 0.000) for 3583 atoms. Found 17 (17 requested) and removed 36 (8 requested) atoms. Cycle 27: After refmac, R = 0.2243 (Rfree = 0.000) for 3557 atoms. Found 16 (16 requested) and removed 15 (8 requested) atoms. Cycle 28: After refmac, R = 0.2141 (Rfree = 0.000) for 3552 atoms. Found 16 (16 requested) and removed 19 (8 requested) atoms. Cycle 29: After refmac, R = 0.1636 (Rfree = 0.000) for 3543 atoms. Found 9 (16 requested) and removed 25 (8 requested) atoms. Cycle 30: After refmac, R = 0.1561 (Rfree = 0.000) for 3524 atoms. Found 6 (16 requested) and removed 14 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.82 3.62 Search for helices and strands: 0 residues in 0 chains, 3662 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 3684 seeds are put forward Round 1: 164 peptides, 32 chains. Longest chain 9 peptides. Score 0.291 Round 2: 187 peptides, 31 chains. Longest chain 14 peptides. Score 0.374 Round 3: 177 peptides, 30 chains. Longest chain 12 peptides. Score 0.358 Round 4: 197 peptides, 31 chains. Longest chain 18 peptides. Score 0.403 Round 5: 195 peptides, 31 chains. Longest chain 14 peptides. Score 0.397 Taking the results from Round 4 Chains 31, Residues 166, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5042 reflections ( 98.94 % complete ) and 8781 restraints for refining 3583 atoms. 8148 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2362 (Rfree = 0.000) for 3583 atoms. Found 17 (17 requested) and removed 24 (8 requested) atoms. Cycle 32: After refmac, R = 0.2191 (Rfree = 0.000) for 3560 atoms. Found 16 (16 requested) and removed 14 (8 requested) atoms. Cycle 33: After refmac, R = 0.2128 (Rfree = 0.000) for 3549 atoms. Found 16 (16 requested) and removed 29 (8 requested) atoms. Cycle 34: After refmac, R = 0.1719 (Rfree = 0.000) for 3526 atoms. Found 14 (16 requested) and removed 11 (8 requested) atoms. Cycle 35: After refmac, R = 0.1623 (Rfree = 0.000) for 3528 atoms. Found 3 (16 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.83 3.63 Search for helices and strands: 0 residues in 0 chains, 3624 seeds are put forward NCS extension: 28 residues added (1 deleted due to clashes), 3652 seeds are put forward Round 1: 154 peptides, 33 chains. Longest chain 9 peptides. Score 0.244 Round 2: 183 peptides, 36 chains. Longest chain 9 peptides. Score 0.297 Round 3: 191 peptides, 34 chains. Longest chain 10 peptides. Score 0.347 Round 4: 187 peptides, 35 chains. Longest chain 10 peptides. Score 0.322 Round 5: 178 peptides, 31 chains. Longest chain 10 peptides. Score 0.347 Taking the results from Round 5 Chains 31, Residues 147, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 5042 reflections ( 98.94 % complete ) and 8740 restraints for refining 3583 atoms. 8164 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2223 (Rfree = 0.000) for 3583 atoms. Found 17 (17 requested) and removed 12 (8 requested) atoms. Cycle 37: After refmac, R = 0.2079 (Rfree = 0.000) for 3571 atoms. Found 17 (17 requested) and removed 13 (8 requested) atoms. Cycle 38: After refmac, R = 0.1692 (Rfree = 0.000) for 3565 atoms. Found 3 (16 requested) and removed 9 (8 requested) atoms. Cycle 39: After refmac, R = 0.1733 (Rfree = 0.000) for 3552 atoms. Found 15 (16 requested) and removed 9 (8 requested) atoms. Cycle 40: After refmac, R = 0.1599 (Rfree = 0.000) for 3555 atoms. Found 6 (16 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.83 3.63 Search for helices and strands: 0 residues in 0 chains, 3664 seeds are put forward NCS extension: 3 residues added (0 deleted due to clashes), 3667 seeds are put forward Round 1: 135 peptides, 28 chains. Longest chain 10 peptides. Score 0.251 Round 2: 144 peptides, 27 chains. Longest chain 11 peptides. Score 0.296 Round 3: 152 peptides, 26 chains. Longest chain 11 peptides. Score 0.335 Round 4: 157 peptides, 28 chains. Longest chain 13 peptides. Score 0.323 Round 5: 151 peptides, 28 chains. Longest chain 10 peptides. Score 0.304 Taking the results from Round 3 Chains 26, Residues 126, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 5042 reflections ( 98.94 % complete ) and 8765 restraints for refining 3582 atoms. 8258 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2094 (Rfree = 0.000) for 3582 atoms. Found 17 (17 requested) and removed 15 (8 requested) atoms. Cycle 42: After refmac, R = 0.2273 (Rfree = 0.000) for 3565 atoms. Found 17 (17 requested) and removed 19 (8 requested) atoms. Cycle 43: After refmac, R = 0.2086 (Rfree = 0.000) for 3551 atoms. Found 16 (16 requested) and removed 22 (8 requested) atoms. Cycle 44: After refmac, R = 0.1641 (Rfree = 0.000) for 3541 atoms. Found 12 (16 requested) and removed 16 (8 requested) atoms. Cycle 45: After refmac, R = 0.1710 (Rfree = 0.000) for 3534 atoms. Found 16 (16 requested) and removed 14 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.86 3.66 Search for helices and strands: 0 residues in 0 chains, 3650 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 3664 seeds are put forward Round 1: 149 peptides, 33 chains. Longest chain 7 peptides. Score 0.227 Round 2: 158 peptides, 30 chains. Longest chain 9 peptides. Score 0.299 Round 3: 162 peptides, 30 chains. Longest chain 10 peptides. Score 0.312 Round 4: 169 peptides, 31 chains. Longest chain 10 peptides. Score 0.320 Round 5: 166 peptides, 31 chains. Longest chain 7 peptides. Score 0.311 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 31, Residues 138, 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 2fno-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5042 reflections ( 98.94 % complete ) and 8879 restraints for refining 3583 atoms. 8358 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2283 (Rfree = 0.000) for 3583 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.2203 (Rfree = 0.000) for 3563 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.2213 (Rfree = 0.000) for 3552 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.1977 (Rfree = 0.000) for 3538 atoms. TimeTaking 42.12