null Sun 23 Dec 22:23:08 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2p7i-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2p7i-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2p7i-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p7i-3.6-parrot-hancs 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/hancs/ArpWArp/wArpResults/WorkingDir/2p7i-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p7i-3.6-parrot-hancs ############### 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 22:23:18 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/hancs/ArpWArp/wArpResults/WorkingDir/2p7i-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p7i-3.6-parrot-hancs/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 346 and 0 Target number of residues in the AU: 346 Target solvent content: 0.6574 Checking the provided sequence file Detected sequence length: 250 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 500 Adjusted target solvent content: 0.50 Input MTZ file: 2p7i-3.6-parrot-hancs.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: 97 Cell parameters: 120.769 120.769 149.904 90.000 90.000 90.000 Input sequence file: 2p7i-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 4000 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: 94.045 3.600 Wilson plot Bfac: 83.07 6704 reflections ( 99.70 % complete ) and 0 restraints for refining 4459 atoms. Observations/parameters ratio is 0.38 ------------------------------------------------------ Starting model: R = 0.3261 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3078 (Rfree = 0.000) for 4459 atoms. Found 17 (28 requested) and removed 25 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.58 3.58 Search for helices and strands: 0 residues in 0 chains, 4542 seeds are put forward NCS extension: 0 residues added, 4542 seeds are put forward Round 1: 217 peptides, 41 chains. Longest chain 12 peptides. Score 0.345 Round 2: 271 peptides, 46 chains. Longest chain 12 peptides. Score 0.440 Round 3: 283 peptides, 39 chains. Longest chain 17 peptides. Score 0.550 Round 4: 279 peptides, 39 chains. Longest chain 15 peptides. Score 0.540 Round 5: 302 peptides, 38 chains. Longest chain 17 peptides. Score 0.603 Taking the results from Round 5 Chains 38, Residues 264, Estimated correctness of the model 15.8 % 2 chains (16 residues) have been docked in sequence ------------------------------------------------------ 6704 reflections ( 99.70 % complete ) and 7941 restraints for refining 3624 atoms. 6872 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2593 (Rfree = 0.000) for 3624 atoms. Found 19 (23 requested) and removed 20 (11 requested) atoms. Cycle 2: After refmac, R = 0.2282 (Rfree = 0.000) for 3549 atoms. Found 4 (23 requested) and removed 13 (11 requested) atoms. Cycle 3: After refmac, R = 0.2266 (Rfree = 0.000) for 3509 atoms. Found 6 (22 requested) and removed 12 (11 requested) atoms. Cycle 4: After refmac, R = 0.2227 (Rfree = 0.000) for 3486 atoms. Found 12 (22 requested) and removed 23 (11 requested) atoms. Cycle 5: After refmac, R = 0.2004 (Rfree = 0.000) for 3467 atoms. Found 3 (22 requested) and removed 16 (11 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.56 3.56 Search for helices and strands: 0 residues in 0 chains, 3569 seeds are put forward NCS extension: 18 residues added (5 deleted due to clashes), 3587 seeds are put forward Round 1: 243 peptides, 42 chains. Longest chain 11 peptides. Score 0.409 Round 2: 275 peptides, 39 chains. Longest chain 22 peptides. Score 0.530 Round 3: 281 peptides, 41 chains. Longest chain 15 peptides. Score 0.523 Round 4: 287 peptides, 38 chains. Longest chain 22 peptides. Score 0.569 Round 5: 306 peptides, 38 chains. Longest chain 21 peptides. Score 0.612 Taking the results from Round 5 Chains 40, Residues 268, Estimated correctness of the model 19.3 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 6704 reflections ( 99.70 % complete ) and 7948 restraints for refining 3588 atoms. 6883 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2450 (Rfree = 0.000) for 3588 atoms. Found 15 (23 requested) and removed 60 (11 requested) atoms. Cycle 7: After refmac, R = 0.2438 (Rfree = 0.000) for 3505 atoms. Found 12 (22 requested) and removed 21 (11 requested) atoms. Cycle 8: After refmac, R = 0.2214 (Rfree = 0.000) for 3469 atoms. Found 11 (22 requested) and removed 15 (11 requested) atoms. Cycle 9: After refmac, R = 0.2227 (Rfree = 0.000) for 3456 atoms. Found 7 (22 requested) and removed 18 (11 requested) atoms. Cycle 10: After refmac, R = 0.2060 (Rfree = 0.000) for 3437 atoms. Found 7 (22 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.55 3.55 Search for helices and strands: 0 residues in 0 chains, 3596 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 3610 seeds are put forward Round 1: 245 peptides, 45 chains. Longest chain 11 peptides. Score 0.378 Round 2: 275 peptides, 46 chains. Longest chain 10 peptides. Score 0.451 Round 3: 288 peptides, 44 chains. Longest chain 14 peptides. Score 0.508 Round 4: 274 peptides, 41 chains. Longest chain 16 peptides. Score 0.505 Round 5: 288 peptides, 41 chains. Longest chain 16 peptides. Score 0.540 Taking the results from Round 5 Chains 42, Residues 247, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 6704 reflections ( 99.70 % complete ) and 8131 restraints for refining 3625 atoms. 7154 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2229 (Rfree = 0.000) for 3625 atoms. Found 8 (23 requested) and removed 20 (11 requested) atoms. Cycle 12: After refmac, R = 0.2106 (Rfree = 0.000) for 3592 atoms. Found 8 (23 requested) and removed 14 (11 requested) atoms. Cycle 13: After refmac, R = 0.1999 (Rfree = 0.000) for 3574 atoms. Found 5 (23 requested) and removed 12 (11 requested) atoms. Cycle 14: After refmac, R = 0.1917 (Rfree = 0.000) for 3564 atoms. Found 2 (22 requested) and removed 12 (11 requested) atoms. Cycle 15: After refmac, R = 0.1877 (Rfree = 0.000) for 3538 atoms. Found 2 (22 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.53 3.53 Search for helices and strands: 0 residues in 0 chains, 3662 seeds are put forward NCS extension: 26 residues added (0 deleted due to clashes), 3688 seeds are put forward Round 1: 233 peptides, 43 chains. Longest chain 11 peptides. Score 0.367 Round 2: 282 peptides, 43 chains. Longest chain 12 peptides. Score 0.504 Round 3: 287 peptides, 45 chains. Longest chain 14 peptides. Score 0.494 Round 4: 288 peptides, 42 chains. Longest chain 14 peptides. Score 0.530 Round 5: 284 peptides, 38 chains. Longest chain 25 peptides. Score 0.562 Taking the results from Round 5 Chains 38, Residues 246, Estimated correctness of the model 0.0 % 2 chains (28 residues) have been docked in sequence ------------------------------------------------------ 6704 reflections ( 99.70 % complete ) and 7961 restraints for refining 3625 atoms. 6915 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2307 (Rfree = 0.000) for 3625 atoms. Found 11 (23 requested) and removed 18 (11 requested) atoms. Cycle 17: After refmac, R = 0.2001 (Rfree = 0.000) for 3590 atoms. Found 5 (23 requested) and removed 14 (11 requested) atoms. Cycle 18: After refmac, R = 0.2018 (Rfree = 0.000) for 3569 atoms. Found 3 (22 requested) and removed 12 (11 requested) atoms. Cycle 19: After refmac, R = 0.1939 (Rfree = 0.000) for 3552 atoms. Found 7 (22 requested) and removed 12 (11 requested) atoms. Cycle 20: After refmac, R = 0.1905 (Rfree = 0.000) for 3541 atoms. Found 8 (22 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.54 3.54 Search for helices and strands: 0 residues in 0 chains, 3649 seeds are put forward NCS extension: 36 residues added (4 deleted due to clashes), 3685 seeds are put forward Round 1: 233 peptides, 48 chains. Longest chain 9 peptides. Score 0.303 Round 2: 244 peptides, 41 chains. Longest chain 15 peptides. Score 0.425 Round 3: 275 peptides, 45 chains. Longest chain 15 peptides. Score 0.463 Round 4: 272 peptides, 46 chains. Longest chain 13 peptides. Score 0.443 Round 5: 258 peptides, 42 chains. Longest chain 14 peptides. Score 0.452 Taking the results from Round 3 Chains 45, Residues 230, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6704 reflections ( 99.70 % complete ) and 8201 restraints for refining 3625 atoms. 7326 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2257 (Rfree = 0.000) for 3625 atoms. Found 14 (23 requested) and removed 16 (11 requested) atoms. Cycle 22: After refmac, R = 0.2151 (Rfree = 0.000) for 3602 atoms. Found 9 (23 requested) and removed 15 (11 requested) atoms. Cycle 23: After refmac, R = 0.2043 (Rfree = 0.000) for 3581 atoms. Found 9 (23 requested) and removed 30 (11 requested) atoms. Cycle 24: After refmac, R = 0.1894 (Rfree = 0.000) for 3551 atoms. Found 5 (22 requested) and removed 21 (11 requested) atoms. Cycle 25: After refmac, R = 0.1949 (Rfree = 0.000) for 3524 atoms. Found 5 (22 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.57 3.57 Search for helices and strands: 0 residues in 0 chains, 3648 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 3664 seeds are put forward Round 1: 219 peptides, 44 chains. Longest chain 9 peptides. Score 0.311 Round 2: 235 peptides, 41 chains. Longest chain 14 peptides. Score 0.399 Round 3: 236 peptides, 41 chains. Longest chain 13 peptides. Score 0.402 Round 4: 239 peptides, 40 chains. Longest chain 12 peptides. Score 0.423 Round 5: 245 peptides, 43 chains. Longest chain 11 peptides. Score 0.403 Taking the results from Round 4 Chains 40, Residues 199, Estimated correctness of the model 0.0 % 4 chains (22 residues) have been docked in sequence ------------------------------------------------------ 6704 reflections ( 99.70 % complete ) and 8207 restraints for refining 3626 atoms. 7369 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2293 (Rfree = 0.000) for 3626 atoms. Found 16 (23 requested) and removed 12 (11 requested) atoms. Cycle 27: After refmac, R = 0.2126 (Rfree = 0.000) for 3607 atoms. Found 17 (23 requested) and removed 13 (11 requested) atoms. Cycle 28: After refmac, R = 0.2053 (Rfree = 0.000) for 3596 atoms. Found 15 (23 requested) and removed 12 (11 requested) atoms. Cycle 29: After refmac, R = 0.1730 (Rfree = 0.000) for 3584 atoms. Found 3 (23 requested) and removed 11 (11 requested) atoms. Cycle 30: After refmac, R = 0.1686 (Rfree = 0.000) for 3569 atoms. Found 0 (22 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.59 3.59 Search for helices and strands: 0 residues in 0 chains, 3652 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 3668 seeds are put forward Round 1: 221 peptides, 45 chains. Longest chain 10 peptides. Score 0.304 Round 2: 249 peptides, 44 chains. Longest chain 11 peptides. Score 0.402 Round 3: 255 peptides, 45 chains. Longest chain 12 peptides. Score 0.407 Round 4: 230 peptides, 42 chains. Longest chain 10 peptides. Score 0.371 Round 5: 220 peptides, 38 chains. Longest chain 12 peptides. Score 0.393 Taking the results from Round 3 Chains 45, Residues 210, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6704 reflections ( 99.70 % complete ) and 8420 restraints for refining 3626 atoms. 7625 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2130 (Rfree = 0.000) for 3626 atoms. Found 16 (23 requested) and removed 12 (11 requested) atoms. Cycle 32: After refmac, R = 0.2034 (Rfree = 0.000) for 3616 atoms. Found 20 (23 requested) and removed 11 (11 requested) atoms. Cycle 33: After refmac, R = 0.2036 (Rfree = 0.000) for 3615 atoms. Found 20 (23 requested) and removed 11 (11 requested) atoms. Cycle 34: After refmac, R = 0.1978 (Rfree = 0.000) for 3615 atoms. Found 14 (23 requested) and removed 14 (11 requested) atoms. Cycle 35: After refmac, R = 0.2062 (Rfree = 0.000) for 3607 atoms. Found 23 (23 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.55 3.55 Search for helices and strands: 0 residues in 0 chains, 3756 seeds are put forward NCS extension: 9 residues added (0 deleted due to clashes), 3765 seeds are put forward Round 1: 186 peptides, 38 chains. Longest chain 12 peptides. Score 0.286 Round 2: 222 peptides, 42 chains. Longest chain 11 peptides. Score 0.347 Round 3: 202 peptides, 37 chains. Longest chain 11 peptides. Score 0.351 Round 4: 207 peptides, 34 chains. Longest chain 14 peptides. Score 0.405 Round 5: 219 peptides, 36 chains. Longest chain 14 peptides. Score 0.415 Taking the results from Round 5 Chains 38, Residues 183, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 6704 reflections ( 99.70 % complete ) and 8434 restraints for refining 3625 atoms. 7704 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2181 (Rfree = 0.000) for 3625 atoms. Found 18 (23 requested) and removed 13 (11 requested) atoms. Cycle 37: After refmac, R = 0.2036 (Rfree = 0.000) for 3606 atoms. Found 10 (23 requested) and removed 13 (11 requested) atoms. Cycle 38: After refmac, R = 0.2158 (Rfree = 0.000) for 3590 atoms. Found 13 (23 requested) and removed 13 (11 requested) atoms. Cycle 39: After refmac, R = 0.2078 (Rfree = 0.000) for 3581 atoms. Found 11 (23 requested) and removed 12 (11 requested) atoms. Cycle 40: After refmac, R = 0.1728 (Rfree = 0.000) for 3572 atoms. Found 1 (22 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.55 3.55 Search for helices and strands: 0 residues in 0 chains, 3639 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 3652 seeds are put forward Round 1: 153 peptides, 31 chains. Longest chain 12 peptides. Score 0.274 Round 2: 196 peptides, 35 chains. Longest chain 18 peptides. Score 0.359 Round 3: 190 peptides, 32 chains. Longest chain 10 peptides. Score 0.381 Round 4: 191 peptides, 29 chains. Longest chain 18 peptides. Score 0.423 Round 5: 185 peptides, 28 chains. Longest chain 15 peptides. Score 0.419 Taking the results from Round 4 Chains 29, Residues 162, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6704 reflections ( 99.70 % complete ) and 8607 restraints for refining 3626 atoms. 7988 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2208 (Rfree = 0.000) for 3626 atoms. Found 16 (23 requested) and removed 16 (11 requested) atoms. Cycle 42: After refmac, R = 0.2260 (Rfree = 0.000) for 3603 atoms. Found 23 (23 requested) and removed 11 (11 requested) atoms. Cycle 43: After refmac, R = 0.2004 (Rfree = 0.000) for 3610 atoms. Found 7 (23 requested) and removed 13 (11 requested) atoms. Cycle 44: After refmac, R = 0.1859 (Rfree = 0.000) for 3597 atoms. Found 9 (23 requested) and removed 14 (11 requested) atoms. Cycle 45: After refmac, R = 0.1961 (Rfree = 0.000) for 3589 atoms. Found 4 (23 requested) and removed 16 (11 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.52 3.52 Search for helices and strands: 0 residues in 0 chains, 3694 seeds are put forward NCS extension: 30 residues added (0 deleted due to clashes), 3724 seeds are put forward Round 1: 139 peptides, 31 chains. Longest chain 8 peptides. Score 0.224 Round 2: 155 peptides, 30 chains. Longest chain 16 peptides. Score 0.296 Round 3: 167 peptides, 34 chains. Longest chain 9 peptides. Score 0.279 Round 4: 169 peptides, 31 chains. Longest chain 16 peptides. Score 0.328 Round 5: 163 peptides, 30 chains. Longest chain 8 peptides. Score 0.322 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 2p7i-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6704 reflections ( 99.70 % complete ) and 8395 restraints for refining 3580 atoms. 7874 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1947 (Rfree = 0.000) for 3580 atoms. Found 0 (22 requested) and removed 11 (11 requested) atoms. Cycle 47: After refmac, R = 0.1946 (Rfree = 0.000) for 3554 atoms. Found 0 (22 requested) and removed 11 (11 requested) atoms. Cycle 48: After refmac, R = 0.2033 (Rfree = 0.000) for 3536 atoms. Found 0 (22 requested) and removed 11 (11 requested) atoms. Cycle 49: After refmac, R = 0.1999 (Rfree = 0.000) for 3519 atoms. Found 0 (22 requested) and removed 11 (11 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:24:48 GMT 2018 Job finished. TimeTaking 61.67 Used memory is bytes: 772200