Mon 24 Dec 00:17:23 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 1vpm-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vpm-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vpm-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vpm-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/1vpm-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vpm-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 ============================================================ Mon 24 Dec 00:17:28 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/1vpm-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vpm-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 327 and 0 Target number of residues in the AU: 327 Target solvent content: 0.6665 Checking the provided sequence file Detected sequence length: 169 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 3 Adjusted target number of residues: 507 Adjusted target solvent content: 0.48 Input MTZ file: 1vpm-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: 24 Cell parameters: 82.941 106.484 120.177 90.000 90.000 90.000 Input sequence file: 1vpm-4.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 4056 target number of atoms Had to go as low as 0.60 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: 79.699 4.001 Wilson plot Bfac: 89.10 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 4611 reflections ( 97.44 % complete ) and 0 restraints for refining 4497 atoms. Observations/parameters ratio is 0.26 ------------------------------------------------------ Starting model: R = 0.3208 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3532 (Rfree = 0.000) for 4497 atoms. Found 21 (21 requested) and removed 33 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.80 3.90 Search for helices and strands: 0 residues in 0 chains, 4560 seeds are put forward NCS extension: 0 residues added, 4560 seeds are put forward Round 1: 155 peptides, 30 chains. Longest chain 12 peptides. Score 0.298 Round 2: 222 peptides, 36 chains. Longest chain 15 peptides. Score 0.429 Round 3: 239 peptides, 35 chains. Longest chain 18 peptides. Score 0.489 Round 4: 243 peptides, 36 chains. Longest chain 15 peptides. Score 0.488 Round 5: 252 peptides, 33 chains. Longest chain 17 peptides. Score 0.547 Taking the results from Round 5 Chains 33, Residues 219, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 4611 reflections ( 97.44 % complete ) and 8482 restraints for refining 3662 atoms. 7602 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2718 (Rfree = 0.000) for 3662 atoms. Found 17 (17 requested) and removed 31 (8 requested) atoms. Cycle 2: After refmac, R = 0.2634 (Rfree = 0.000) for 3558 atoms. Found 17 (17 requested) and removed 25 (8 requested) atoms. Cycle 3: After refmac, R = 0.2388 (Rfree = 0.000) for 3482 atoms. Found 16 (16 requested) and removed 20 (8 requested) atoms. Cycle 4: After refmac, R = 0.2378 (Rfree = 0.000) for 3438 atoms. Found 16 (16 requested) and removed 37 (8 requested) atoms. Cycle 5: After refmac, R = 0.2223 (Rfree = 0.000) for 3393 atoms. Found 12 (16 requested) and removed 18 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.75 3.85 Search for helices and strands: 0 residues in 0 chains, 3525 seeds are put forward NCS extension: 25 residues added (1 deleted due to clashes), 3550 seeds are put forward Round 1: 181 peptides, 32 chains. Longest chain 12 peptides. Score 0.356 Round 2: 224 peptides, 33 chains. Longest chain 15 peptides. Score 0.473 Round 3: 241 peptides, 33 chains. Longest chain 20 peptides. Score 0.518 Round 4: 222 peptides, 34 chains. Longest chain 15 peptides. Score 0.454 Round 5: 233 peptides, 34 chains. Longest chain 16 peptides. Score 0.485 Taking the results from Round 3 Chains 33, Residues 208, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4611 reflections ( 97.44 % complete ) and 7557 restraints for refining 3299 atoms. 6758 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2361 (Rfree = 0.000) for 3299 atoms. Found 15 (15 requested) and removed 47 (7 requested) atoms. Cycle 7: After refmac, R = 0.2502 (Rfree = 0.000) for 3236 atoms. Found 15 (15 requested) and removed 33 (7 requested) atoms. Cycle 8: After refmac, R = 0.2172 (Rfree = 0.000) for 3197 atoms. Found 15 (15 requested) and removed 18 (7 requested) atoms. Cycle 9: After refmac, R = 0.1707 (Rfree = 0.000) for 3175 atoms. Found 7 (15 requested) and removed 16 (7 requested) atoms. Cycle 10: After refmac, R = 0.1520 (Rfree = 0.000) for 3156 atoms. Found 2 (15 requested) and removed 14 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.79 3.89 Search for helices and strands: 0 residues in 0 chains, 3280 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 3301 seeds are put forward Round 1: 191 peptides, 35 chains. Longest chain 15 peptides. Score 0.347 Round 2: 239 peptides, 37 chains. Longest chain 16 peptides. Score 0.465 Round 3: 240 peptides, 35 chains. Longest chain 17 peptides. Score 0.492 Round 4: 253 peptides, 34 chains. Longest chain 19 peptides. Score 0.538 Round 5: 239 peptides, 34 chains. Longest chain 23 peptides. Score 0.501 Taking the results from Round 4 Chains 36, Residues 219, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 4611 reflections ( 97.44 % complete ) and 7415 restraints for refining 3337 atoms. 6535 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2300 (Rfree = 0.000) for 3337 atoms. Found 15 (15 requested) and removed 31 (7 requested) atoms. Cycle 12: After refmac, R = 0.2148 (Rfree = 0.000) for 3290 atoms. Found 15 (15 requested) and removed 15 (7 requested) atoms. Cycle 13: After refmac, R = 0.2067 (Rfree = 0.000) for 3260 atoms. Found 15 (15 requested) and removed 19 (7 requested) atoms. Cycle 14: After refmac, R = 0.1982 (Rfree = 0.000) for 3244 atoms. Found 15 (15 requested) and removed 18 (7 requested) atoms. Cycle 15: After refmac, R = 0.1885 (Rfree = 0.000) for 3224 atoms. Found 15 (15 requested) and removed 12 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.74 3.84 Search for helices and strands: 0 residues in 0 chains, 3381 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 3399 seeds are put forward Round 1: 183 peptides, 34 chains. Longest chain 13 peptides. Score 0.335 Round 2: 223 peptides, 35 chains. Longest chain 17 peptides. Score 0.445 Round 3: 222 peptides, 35 chains. Longest chain 19 peptides. Score 0.442 Round 4: 215 peptides, 30 chains. Longest chain 23 peptides. Score 0.485 Round 5: 231 peptides, 32 chains. Longest chain 19 peptides. Score 0.504 Taking the results from Round 5 Chains 32, Residues 199, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4611 reflections ( 97.44 % complete ) and 7856 restraints for refining 3394 atoms. 7092 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2116 (Rfree = 0.000) for 3394 atoms. Found 16 (16 requested) and removed 27 (8 requested) atoms. Cycle 17: After refmac, R = 0.1819 (Rfree = 0.000) for 3359 atoms. Found 16 (16 requested) and removed 17 (8 requested) atoms. Cycle 18: After refmac, R = 0.1912 (Rfree = 0.000) for 3339 atoms. Found 15 (15 requested) and removed 15 (7 requested) atoms. Cycle 19: After refmac, R = 0.1701 (Rfree = 0.000) for 3320 atoms. Found 15 (15 requested) and removed 12 (7 requested) atoms. Cycle 20: After refmac, R = 0.1788 (Rfree = 0.000) for 3307 atoms. Found 15 (15 requested) and removed 13 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.75 3.85 Search for helices and strands: 0 residues in 0 chains, 3458 seeds are put forward NCS extension: 25 residues added (1 deleted due to clashes), 3483 seeds are put forward Round 1: 188 peptides, 36 chains. Longest chain 11 peptides. Score 0.323 Round 2: 223 peptides, 39 chains. Longest chain 12 peptides. Score 0.393 Round 3: 238 peptides, 36 chains. Longest chain 16 peptides. Score 0.475 Round 4: 231 peptides, 36 chains. Longest chain 12 peptides. Score 0.455 Round 5: 244 peptides, 35 chains. Longest chain 14 peptides. Score 0.503 Taking the results from Round 5 Chains 37, Residues 209, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 4611 reflections ( 97.44 % complete ) and 8192 restraints for refining 3571 atoms. 7348 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1778 (Rfree = 0.000) for 3571 atoms. Found 10 (16 requested) and removed 25 (8 requested) atoms. Cycle 22: After refmac, R = 0.1878 (Rfree = 0.000) for 3522 atoms. Found 16 (16 requested) and removed 13 (8 requested) atoms. Cycle 23: After refmac, R = 0.1792 (Rfree = 0.000) for 3500 atoms. Found 13 (16 requested) and removed 14 (8 requested) atoms. Cycle 24: After refmac, R = 0.1344 (Rfree = 0.000) for 3482 atoms. Found 0 (16 requested) and removed 12 (8 requested) atoms. Cycle 25: After refmac, R = 0.1630 (Rfree = 0.000) for 3454 atoms. Found 14 (16 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.71 3.81 Search for helices and strands: 0 residues in 0 chains, 3577 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 3589 seeds are put forward Round 1: 163 peptides, 32 chains. Longest chain 8 peptides. Score 0.296 Round 2: 195 peptides, 33 chains. Longest chain 13 peptides. Score 0.387 Round 3: 202 peptides, 31 chains. Longest chain 17 peptides. Score 0.435 Round 4: 209 peptides, 35 chains. Longest chain 12 peptides. Score 0.403 Round 5: 229 peptides, 36 chains. Longest chain 14 peptides. Score 0.449 Taking the results from Round 5 Chains 36, Residues 193, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4611 reflections ( 97.44 % complete ) and 8666 restraints for refining 3636 atoms. 7930 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2142 (Rfree = 0.000) for 3636 atoms. Found 17 (17 requested) and removed 34 (8 requested) atoms. Cycle 27: After refmac, R = 0.1794 (Rfree = 0.000) for 3581 atoms. Found 15 (17 requested) and removed 18 (8 requested) atoms. Cycle 28: After refmac, R = 0.1873 (Rfree = 0.000) for 3557 atoms. Found 16 (16 requested) and removed 38 (8 requested) atoms. Cycle 29: After refmac, R = 0.1795 (Rfree = 0.000) for 3524 atoms. Found 16 (16 requested) and removed 16 (8 requested) atoms. Cycle 30: After refmac, R = 0.1846 (Rfree = 0.000) for 3515 atoms. Found 16 (16 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.72 3.82 Search for helices and strands: 0 residues in 0 chains, 3648 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 3661 seeds are put forward Round 1: 165 peptides, 33 chains. Longest chain 10 peptides. Score 0.289 Round 2: 195 peptides, 36 chains. Longest chain 11 peptides. Score 0.346 Round 3: 204 peptides, 36 chains. Longest chain 11 peptides. Score 0.374 Round 4: 209 peptides, 35 chains. Longest chain 16 peptides. Score 0.403 Round 5: 212 peptides, 34 chains. Longest chain 15 peptides. Score 0.425 Taking the results from Round 5 Chains 34, Residues 178, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4611 reflections ( 97.44 % complete ) and 8525 restraints for refining 3611 atoms. 7847 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2075 (Rfree = 0.000) for 3611 atoms. Found 17 (17 requested) and removed 20 (8 requested) atoms. Cycle 32: After refmac, R = 0.2025 (Rfree = 0.000) for 3558 atoms. Found 17 (17 requested) and removed 49 (8 requested) atoms. Cycle 33: After refmac, R = 0.1847 (Rfree = 0.000) for 3510 atoms. Found 16 (16 requested) and removed 14 (8 requested) atoms. Cycle 34: After refmac, R = 0.1363 (Rfree = 0.000) for 3496 atoms. Found 4 (16 requested) and removed 9 (8 requested) atoms. Cycle 35: After refmac, R = 0.1238 (Rfree = 0.000) for 3479 atoms. Found 1 (16 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.76 3.86 Search for helices and strands: 0 residues in 0 chains, 3594 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 3612 seeds are put forward Round 1: 165 peptides, 34 chains. Longest chain 8 peptides. Score 0.274 Round 2: 166 peptides, 33 chains. Longest chain 9 peptides. Score 0.292 Round 3: 162 peptides, 29 chains. Longest chain 12 peptides. Score 0.337 Round 4: 177 peptides, 28 chains. Longest chain 17 peptides. Score 0.399 Round 5: 169 peptides, 30 chains. Longest chain 13 peptides. Score 0.346 Taking the results from Round 4 Chains 28, Residues 149, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 4611 reflections ( 97.44 % complete ) and 8474 restraints for refining 3570 atoms. 7854 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1862 (Rfree = 0.000) for 3570 atoms. Found 12 (16 requested) and removed 22 (8 requested) atoms. Cycle 37: After refmac, R = 0.1887 (Rfree = 0.000) for 3543 atoms. Found 16 (16 requested) and removed 34 (8 requested) atoms. Cycle 38: After refmac, R = 0.1639 (Rfree = 0.000) for 3517 atoms. Found 16 (16 requested) and removed 13 (8 requested) atoms. Cycle 39: After refmac, R = 0.1157 (Rfree = 0.000) for 3517 atoms. Found 3 (16 requested) and removed 9 (8 requested) atoms. Cycle 40: After refmac, R = 0.1025 (Rfree = 0.000) for 3508 atoms. Found 0 (16 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.75 3.85 Search for helices and strands: 0 residues in 0 chains, 3592 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 3616 seeds are put forward Round 1: 153 peptides, 34 chains. Longest chain 6 peptides. Score 0.231 Round 2: 178 peptides, 36 chains. Longest chain 7 peptides. Score 0.290 Round 3: 191 peptides, 36 chains. Longest chain 9 peptides. Score 0.333 Round 4: 182 peptides, 33 chains. Longest chain 13 peptides. Score 0.346 Round 5: 184 peptides, 32 chains. Longest chain 11 peptides. Score 0.366 Taking the results from Round 5 Chains 32, Residues 152, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4611 reflections ( 97.44 % complete ) and 8854 restraints for refining 3661 atoms. 8278 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1751 (Rfree = 0.000) for 3661 atoms. Found 14 (17 requested) and removed 47 (8 requested) atoms. Cycle 42: After refmac, R = 0.1606 (Rfree = 0.000) for 3595 atoms. Found 12 (17 requested) and removed 25 (8 requested) atoms. Cycle 43: After refmac, R = 0.1661 (Rfree = 0.000) for 3574 atoms. Found 17 (17 requested) and removed 21 (8 requested) atoms. Cycle 44: After refmac, R = 0.1876 (Rfree = 0.000) for 3563 atoms. Found 16 (16 requested) and removed 21 (8 requested) atoms. Cycle 45: After refmac, R = 0.1609 (Rfree = 0.000) for 3553 atoms. Found 16 (16 requested) and removed 17 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.75 3.85 Search for helices and strands: 0 residues in 0 chains, 3654 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 3667 seeds are put forward Round 1: 113 peptides, 25 chains. Longest chain 7 peptides. Score 0.221 Round 2: 141 peptides, 27 chains. Longest chain 13 peptides. Score 0.294 Round 3: 147 peptides, 28 chains. Longest chain 7 peptides. Score 0.300 Round 4: 142 peptides, 25 chains. Longest chain 13 peptides. Score 0.328 Round 5: 143 peptides, 26 chains. Longest chain 8 peptides. Score 0.317 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 25, Residues 117, 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 1vpm-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4611 reflections ( 97.44 % complete ) and 8609 restraints for refining 3527 atoms. 8166 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1947 (Rfree = 0.000) for 3527 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.1658 (Rfree = 0.000) for 3502 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.1642 (Rfree = 0.000) for 3482 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.1085 (Rfree = 0.000) for 3467 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Writing output files ... TimeTaking 36.47