Mon 24 Dec 07:34:55 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 1vpm-4.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vpm-4.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vpm-4.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vpm-4.0-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/1vpm-4.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vpm-4.0-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 07:35:00 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/1vpm-4.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vpm-4.0-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 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-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: 24 Cell parameters: 82.941 106.484 120.177 90.000 90.000 90.000 Input sequence file: 1vpm-4.0-parrot-noncs.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 4506 atoms. Observations/parameters ratio is 0.26 ------------------------------------------------------ Starting model: R = 0.3265 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3533 (Rfree = 0.000) for 4506 atoms. Found 19 (21 requested) and removed 291 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.81 3.91 Search for helices and strands: 0 residues in 0 chains, 4266 seeds are put forward NCS extension: 0 residues added, 4266 seeds are put forward Round 1: 112 peptides, 25 chains. Longest chain 8 peptides. Score 0.217 Round 2: 154 peptides, 31 chains. Longest chain 8 peptides. Score 0.280 Round 3: 170 peptides, 33 chains. Longest chain 8 peptides. Score 0.306 Round 4: 185 peptides, 34 chains. Longest chain 10 peptides. Score 0.341 Round 5: 174 peptides, 29 chains. Longest chain 15 peptides. Score 0.376 Taking the results from Round 5 Chains 29, Residues 145, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4611 reflections ( 97.44 % complete ) and 9036 restraints for refining 3663 atoms. 8485 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3199 (Rfree = 0.000) for 3663 atoms. Found 17 (17 requested) and removed 104 (8 requested) atoms. Cycle 2: After refmac, R = 0.2716 (Rfree = 0.000) for 3523 atoms. Found 10 (16 requested) and removed 45 (8 requested) atoms. Cycle 3: After refmac, R = 0.2612 (Rfree = 0.000) for 3461 atoms. Found 12 (16 requested) and removed 24 (8 requested) atoms. Cycle 4: After refmac, R = 0.2053 (Rfree = 0.000) for 3436 atoms. Found 4 (16 requested) and removed 14 (8 requested) atoms. Cycle 5: After refmac, R = 0.2538 (Rfree = 0.000) for 3416 atoms. Found 8 (16 requested) and removed 18 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.71 3.81 Search for helices and strands: 0 residues in 0 chains, 3512 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 3525 seeds are put forward Round 1: 159 peptides, 34 chains. Longest chain 9 peptides. Score 0.253 Round 2: 219 peptides, 36 chains. Longest chain 14 peptides. Score 0.420 Round 3: 230 peptides, 36 chains. Longest chain 21 peptides. Score 0.452 Round 4: 242 peptides, 35 chains. Longest chain 15 peptides. Score 0.498 Round 5: 237 peptides, 32 chains. Longest chain 21 peptides. Score 0.520 Taking the results from Round 5 Chains 34, Residues 205, Estimated correctness of the model 0.0 % 3 chains (27 residues) have been docked in sequence ------------------------------------------------------ 4611 reflections ( 97.44 % complete ) and 7406 restraints for refining 3350 atoms. 6524 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2270 (Rfree = 0.000) for 3350 atoms. Found 13 (15 requested) and removed 142 (7 requested) atoms. Cycle 7: After refmac, R = 0.2164 (Rfree = 0.000) for 3194 atoms. Found 15 (15 requested) and removed 26 (7 requested) atoms. Cycle 8: After refmac, R = 0.2103 (Rfree = 0.000) for 3155 atoms. Found 13 (15 requested) and removed 17 (7 requested) atoms. Cycle 9: After refmac, R = 0.1968 (Rfree = 0.000) for 3139 atoms. Found 13 (14 requested) and removed 12 (7 requested) atoms. Cycle 10: After refmac, R = 0.2001 (Rfree = 0.000) for 3136 atoms. Found 14 (14 requested) and removed 19 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.76 3.86 Search for helices and strands: 0 residues in 0 chains, 3239 seeds are put forward NCS extension: 24 residues added (2 deleted due to clashes), 3263 seeds are put forward Round 1: 223 peptides, 42 chains. Longest chain 14 peptides. Score 0.354 Round 2: 236 peptides, 39 chains. Longest chain 15 peptides. Score 0.432 Round 3: 232 peptides, 37 chains. Longest chain 14 peptides. Score 0.445 Round 4: 226 peptides, 34 chains. Longest chain 13 peptides. Score 0.466 Round 5: 242 peptides, 35 chains. Longest chain 14 peptides. Score 0.498 Taking the results from Round 5 Chains 36, Residues 207, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4611 reflections ( 97.44 % complete ) and 7669 restraints for refining 3392 atoms. 6847 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2194 (Rfree = 0.000) for 3392 atoms. Found 14 (16 requested) and removed 45 (8 requested) atoms. Cycle 12: After refmac, R = 0.2076 (Rfree = 0.000) for 3317 atoms. Found 12 (15 requested) and removed 16 (7 requested) atoms. Cycle 13: After refmac, R = 0.2008 (Rfree = 0.000) for 3289 atoms. Found 7 (15 requested) and removed 20 (7 requested) atoms. Cycle 14: After refmac, R = 0.1907 (Rfree = 0.000) for 3259 atoms. Found 15 (15 requested) and removed 18 (7 requested) atoms. Cycle 15: After refmac, R = 0.1715 (Rfree = 0.000) for 3245 atoms. Found 9 (15 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.76 3.86 Search for helices and strands: 0 residues in 0 chains, 3385 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 3399 seeds are put forward Round 1: 206 peptides, 40 chains. Longest chain 10 peptides. Score 0.327 Round 2: 232 peptides, 38 chains. Longest chain 12 peptides. Score 0.433 Round 3: 227 peptides, 35 chains. Longest chain 17 peptides. Score 0.456 Round 4: 214 peptides, 32 chains. Longest chain 12 peptides. Score 0.457 Round 5: 230 peptides, 31 chains. Longest chain 17 peptides. Score 0.513 Taking the results from Round 5 Chains 31, Residues 199, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 4611 reflections ( 97.44 % complete ) and 7871 restraints for refining 3439 atoms. 7094 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2333 (Rfree = 0.000) for 3439 atoms. Found 16 (16 requested) and removed 44 (8 requested) atoms. Cycle 17: After refmac, R = 0.2036 (Rfree = 0.000) for 3374 atoms. Found 16 (16 requested) and removed 31 (8 requested) atoms. Cycle 18: After refmac, R = 0.2086 (Rfree = 0.000) for 3335 atoms. Found 15 (15 requested) and removed 18 (7 requested) atoms. Cycle 19: After refmac, R = 0.1648 (Rfree = 0.000) for 3318 atoms. Found 13 (15 requested) and removed 25 (7 requested) atoms. Cycle 20: After refmac, R = 0.1969 (Rfree = 0.000) for 3296 atoms. Found 15 (15 requested) and removed 26 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.66 3.76 Search for helices and strands: 0 residues in 0 chains, 3442 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 3458 seeds are put forward Round 1: 183 peptides, 38 chains. Longest chain 8 peptides. Score 0.278 Round 2: 211 peptides, 35 chains. Longest chain 13 peptides. Score 0.409 Round 3: 216 peptides, 36 chains. Longest chain 14 peptides. Score 0.411 Round 4: 212 peptides, 34 chains. Longest chain 17 peptides. Score 0.425 Round 5: 214 peptides, 33 chains. Longest chain 16 peptides. Score 0.444 Taking the results from Round 5 Chains 33, Residues 181, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4611 reflections ( 97.44 % complete ) and 8043 restraints for refining 3509 atoms. 7352 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1935 (Rfree = 0.000) for 3509 atoms. Found 15 (16 requested) and removed 53 (8 requested) atoms. Cycle 22: After refmac, R = 0.1801 (Rfree = 0.000) for 3445 atoms. Found 16 (16 requested) and removed 29 (8 requested) atoms. Cycle 23: After refmac, R = 0.1914 (Rfree = 0.000) for 3419 atoms. Found 16 (16 requested) and removed 28 (8 requested) atoms. Cycle 24: After refmac, R = 0.1612 (Rfree = 0.000) for 3403 atoms. Found 16 (16 requested) and removed 22 (8 requested) atoms. Cycle 25: After refmac, R = 0.2044 (Rfree = 0.000) for 3388 atoms. Found 16 (16 requested) and removed 16 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.71 3.81 Search for helices and strands: 0 residues in 0 chains, 3524 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 3537 seeds are put forward Round 1: 189 peptides, 36 chains. Longest chain 11 peptides. Score 0.326 Round 2: 217 peptides, 33 chains. Longest chain 16 peptides. Score 0.453 Round 3: 217 peptides, 32 chains. Longest chain 13 peptides. Score 0.465 Round 4: 211 peptides, 34 chains. Longest chain 14 peptides. Score 0.422 Round 5: 220 peptides, 35 chains. Longest chain 15 peptides. Score 0.436 Taking the results from Round 3 Chains 32, Residues 185, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4611 reflections ( 97.44 % complete ) and 7947 restraints for refining 3471 atoms. 7239 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2018 (Rfree = 0.000) for 3471 atoms. Found 16 (16 requested) and removed 26 (8 requested) atoms. Cycle 27: After refmac, R = 0.1991 (Rfree = 0.000) for 3449 atoms. Found 16 (16 requested) and removed 32 (8 requested) atoms. Cycle 28: After refmac, R = 0.1855 (Rfree = 0.000) for 3418 atoms. Found 16 (16 requested) and removed 17 (8 requested) atoms. Cycle 29: After refmac, R = 0.2152 (Rfree = 0.000) for 3406 atoms. Found 16 (16 requested) and removed 25 (8 requested) atoms. Cycle 30: After refmac, R = 0.1931 (Rfree = 0.000) for 3382 atoms. Found 16 (16 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.82 3.92 Search for helices and strands: 0 residues in 0 chains, 3519 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 3537 seeds are put forward Round 1: 134 peptides, 29 chains. Longest chain 10 peptides. Score 0.238 Round 2: 185 peptides, 35 chains. Longest chain 16 peptides. Score 0.327 Round 3: 190 peptides, 31 chains. Longest chain 17 peptides. Score 0.399 Round 4: 192 peptides, 29 chains. Longest chain 20 peptides. Score 0.431 Round 5: 187 peptides, 28 chains. Longest chain 23 peptides. Score 0.430 Taking the results from Round 4 Chains 29, Residues 163, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4611 reflections ( 97.44 % complete ) and 8052 restraints for refining 3431 atoms. 7429 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2089 (Rfree = 0.000) for 3431 atoms. Found 16 (16 requested) and removed 41 (8 requested) atoms. Cycle 32: After refmac, R = 0.2080 (Rfree = 0.000) for 3389 atoms. Found 16 (16 requested) and removed 25 (8 requested) atoms. Cycle 33: After refmac, R = 0.1877 (Rfree = 0.000) for 3371 atoms. Found 16 (16 requested) and removed 15 (8 requested) atoms. Cycle 34: After refmac, R = 0.1881 (Rfree = 0.000) for 3362 atoms. Found 16 (16 requested) and removed 13 (8 requested) atoms. Cycle 35: After refmac, R = 0.2328 (Rfree = 0.000) for 3351 atoms. Found 15 (15 requested) and removed 23 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.69 3.79 Search for helices and strands: 0 residues in 0 chains, 3466 seeds are put forward NCS extension: 27 residues added (0 deleted due to clashes), 3493 seeds are put forward Round 1: 143 peptides, 31 chains. Longest chain 10 peptides. Score 0.240 Round 2: 183 peptides, 35 chains. Longest chain 15 peptides. Score 0.321 Round 3: 181 peptides, 33 chains. Longest chain 12 peptides. Score 0.342 Round 4: 186 peptides, 30 chains. Longest chain 17 peptides. Score 0.400 Round 5: 183 peptides, 30 chains. Longest chain 13 peptides. Score 0.391 Taking the results from Round 4 Chains 30, Residues 156, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4611 reflections ( 97.44 % complete ) and 7964 restraints for refining 3428 atoms. 7370 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2231 (Rfree = 0.000) for 3428 atoms. Found 16 (16 requested) and removed 42 (8 requested) atoms. Cycle 37: After refmac, R = 0.2076 (Rfree = 0.000) for 3389 atoms. Found 12 (16 requested) and removed 33 (8 requested) atoms. Cycle 38: After refmac, R = 0.2088 (Rfree = 0.000) for 3356 atoms. Found 15 (15 requested) and removed 24 (7 requested) atoms. Cycle 39: After refmac, R = 0.1840 (Rfree = 0.000) for 3333 atoms. Found 15 (15 requested) and removed 15 (7 requested) atoms. Cycle 40: After refmac, R = 0.1862 (Rfree = 0.000) for 3321 atoms. Found 15 (15 requested) and removed 13 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.71 3.81 Search for helices and strands: 0 residues in 0 chains, 3419 seeds are put forward NCS extension: 34 residues added (1 deleted due to clashes), 3453 seeds are put forward Round 1: 131 peptides, 29 chains. Longest chain 9 peptides. Score 0.226 Round 2: 176 peptides, 33 chains. Longest chain 12 peptides. Score 0.326 Round 3: 167 peptides, 28 chains. Longest chain 21 peptides. Score 0.368 Round 4: 183 peptides, 31 chains. Longest chain 17 peptides. Score 0.377 Round 5: 185 peptides, 29 chains. Longest chain 21 peptides. Score 0.410 Taking the results from Round 5 Chains 30, Residues 156, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4611 reflections ( 97.44 % complete ) and 7585 restraints for refining 3386 atoms. 6964 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2178 (Rfree = 0.000) for 3386 atoms. Found 16 (16 requested) and removed 54 (8 requested) atoms. Cycle 42: After refmac, R = 0.1789 (Rfree = 0.000) for 3337 atoms. Found 15 (15 requested) and removed 17 (7 requested) atoms. Cycle 43: After refmac, R = 0.1938 (Rfree = 0.000) for 3327 atoms. Found 15 (15 requested) and removed 22 (7 requested) atoms. Cycle 44: After refmac, R = 0.1898 (Rfree = 0.000) for 3311 atoms. Found 15 (15 requested) and removed 14 (7 requested) atoms. Cycle 45: After refmac, R = 0.1943 (Rfree = 0.000) for 3301 atoms. Found 15 (15 requested) and removed 19 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.70 3.80 Search for helices and strands: 0 residues in 0 chains, 3401 seeds are put forward NCS extension: 24 residues added (2 deleted due to clashes), 3425 seeds are put forward Round 1: 99 peptides, 22 chains. Longest chain 7 peptides. Score 0.215 Round 2: 128 peptides, 24 chains. Longest chain 17 peptides. Score 0.294 Round 3: 138 peptides, 24 chains. Longest chain 15 peptides. Score 0.330 Round 4: 136 peptides, 22 chains. Longest chain 14 peptides. Score 0.353 Round 5: 139 peptides, 24 chains. Longest chain 14 peptides. Score 0.333 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 23, Residues 114, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence Sequence coverage is 9 % 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 7704 restraints for refining 3341 atoms. 7238 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2106 (Rfree = 0.000) for 3341 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.2103 (Rfree = 0.000) for 3327 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.2065 (Rfree = 0.000) for 3315 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.2079 (Rfree = 0.000) for 3295 atoms. TimeTaking 41.98