null Sun 23 Dec 22:23:02 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 1vra-2.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vra-2.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vra-2.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vra-2.2-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/1vra-2.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vra-2.2-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 22:23:12 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/1vra-2.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vra-2.2-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 558 and 0 Target number of residues in the AU: 558 Target solvent content: 0.4558 Checking the provided sequence file Detected sequence length: 423 Maximum limit of NCS related copies: 30 Number of NCS-related molecules: 1 Adjusted target number of residues: 423 Adjusted target solvent content: 0.59 Input MTZ file: 1vra-2.2-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: 92 Cell parameters: 70.658 70.658 222.292 90.000 90.000 90.000 Input sequence file: 1vra-2.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 3384 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 1 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 Loops will be built when appropriate and at the last cycle Resolution range: 29.814 2.200 Wilson plot Bfac: 15.45 29472 reflections ( 99.51 % complete ) and 0 restraints for refining 3766 atoms. Observations/parameters ratio is 1.96 ------------------------------------------------------ Starting model: R = 0.3484 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2897 (Rfree = 0.000) for 3766 atoms. Found 98 (98 requested) and removed 50 (49 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.88 1.67 Round 1: 328 peptides, 35 chains. Longest chain 31 peptides. Score 0.677 Round 2: 364 peptides, 19 chains. Longest chain 51 peptides. Score 0.836 Round 3: 386 peptides, 13 chains. Longest chain 73 peptides. Score 0.884 Round 4: 396 peptides, 6 chains. Longest chain 117 peptides. Score 0.919 Round 5: 391 peptides, 10 chains. Longest chain 72 peptides. Score 0.901 Taking the results from Round 4 Chains 8, Residues 390, Estimated correctness of the model 99.0 % 6 chains (384 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 89 A and 92 A Built loop between residues 50 B and 57 B Built loop between residues 132 B and 136 B Built loop between residues 180 B and 183 B 2 chains (397 residues) following loop building 2 chains (397 residues) in sequence following loop building ------------------------------------------------------ 29472 reflections ( 99.51 % complete ) and 3354 restraints for refining 3525 atoms. 369 conditional restraints added. Observations/parameters ratio is 2.09 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3227 (Rfree = 0.000) for 3525 atoms. Found 92 (92 requested) and removed 58 (46 requested) atoms. Cycle 2: After refmac, R = 0.2885 (Rfree = 0.000) for 3542 atoms. Found 57 (90 requested) and removed 46 (46 requested) atoms. Cycle 3: After refmac, R = 0.2654 (Rfree = 0.000) for 3532 atoms. Found 60 (88 requested) and removed 45 (46 requested) atoms. Cycle 4: After refmac, R = 0.2549 (Rfree = 0.000) for 3539 atoms. Found 49 (86 requested) and removed 21 (46 requested) atoms. Cycle 5: After refmac, R = 0.2468 (Rfree = 0.000) for 3554 atoms. Found 48 (87 requested) and removed 26 (46 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.87 1.66 Round 1: 396 peptides, 5 chains. Longest chain 122 peptides. Score 0.923 Round 2: 397 peptides, 4 chains. Longest chain 180 peptides. Score 0.927 Round 3: 396 peptides, 6 chains. Longest chain 188 peptides. Score 0.919 Round 4: 395 peptides, 7 chains. Longest chain 95 peptides. Score 0.915 Round 5: 387 peptides, 9 chains. Longest chain 124 peptides. Score 0.902 Taking the results from Round 2 Chains 4, Residues 393, Estimated correctness of the model 99.2 % 4 chains (393 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 135 A and 138 A Built loop between residues 180 B and 183 B 2 chains (397 residues) following loop building 2 chains (397 residues) in sequence following loop building ------------------------------------------------------ 29472 reflections ( 99.51 % complete ) and 3334 restraints for refining 3482 atoms. 349 conditional restraints added. Observations/parameters ratio is 2.12 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2662 (Rfree = 0.000) for 3482 atoms. Found 78 (83 requested) and removed 51 (45 requested) atoms. Cycle 7: After refmac, R = 0.2476 (Rfree = 0.000) for 3508 atoms. Found 59 (82 requested) and removed 26 (45 requested) atoms. Cycle 8: After refmac, R = 0.2387 (Rfree = 0.000) for 3537 atoms. Found 59 (83 requested) and removed 31 (46 requested) atoms. Cycle 9: After refmac, R = 0.2357 (Rfree = 0.000) for 3563 atoms. Found 51 (82 requested) and removed 37 (46 requested) atoms. Cycle 10: After refmac, R = 0.2312 (Rfree = 0.000) for 3573 atoms. Found 49 (80 requested) and removed 41 (46 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.88 1.67 Round 1: 393 peptides, 6 chains. Longest chain 180 peptides. Score 0.918 Round 2: 396 peptides, 4 chains. Longest chain 187 peptides. Score 0.927 Round 3: 393 peptides, 6 chains. Longest chain 114 peptides. Score 0.918 Round 4: 393 peptides, 7 chains. Longest chain 153 peptides. Score 0.914 Round 5: 397 peptides, 5 chains. Longest chain 180 peptides. Score 0.924 Taking the results from Round 2 Chains 4, Residues 392, Estimated correctness of the model 99.2 % 4 chains (392 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 128 B and 131 B Built loop between residues 179 B and 182 B 2 chains (396 residues) following loop building 2 chains (396 residues) in sequence following loop building ------------------------------------------------------ 29472 reflections ( 99.51 % complete ) and 3376 restraints for refining 3499 atoms. 399 conditional restraints added. Observations/parameters ratio is 2.11 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2408 (Rfree = 0.000) for 3499 atoms. Found 76 (76 requested) and removed 50 (45 requested) atoms. Cycle 12: After refmac, R = 0.2393 (Rfree = 0.000) for 3523 atoms. Found 53 (75 requested) and removed 46 (45 requested) atoms. Cycle 13: After refmac, R = 0.2323 (Rfree = 0.000) for 3529 atoms. Found 64 (74 requested) and removed 32 (46 requested) atoms. Cycle 14: After refmac, R = 0.2331 (Rfree = 0.000) for 3561 atoms. Found 45 (74 requested) and removed 46 (46 requested) atoms. Cycle 15: After refmac, R = 0.2287 (Rfree = 0.000) for 3557 atoms. Found 55 (72 requested) and removed 37 (46 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.90 1.68 Round 1: 386 peptides, 8 chains. Longest chain 75 peptides. Score 0.906 Round 2: 392 peptides, 5 chains. Longest chain 110 peptides. Score 0.921 Round 3: 394 peptides, 7 chains. Longest chain 180 peptides. Score 0.914 Round 4: 396 peptides, 5 chains. Longest chain 128 peptides. Score 0.923 Round 5: 395 peptides, 8 chains. Longest chain 153 peptides. Score 0.911 Taking the results from Round 4 Chains 5, Residues 391, Estimated correctness of the model 99.1 % 5 chains (391 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 135 A and 138 A Built loop between residues 128 B and 131 B Built loop between residues 179 B and 182 B 2 chains (397 residues) following loop building 2 chains (397 residues) in sequence following loop building ------------------------------------------------------ 29472 reflections ( 99.51 % complete ) and 3319 restraints for refining 3475 atoms. 334 conditional restraints added. Observations/parameters ratio is 2.12 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2426 (Rfree = 0.000) for 3475 atoms. Found 68 (68 requested) and removed 49 (45 requested) atoms. Cycle 17: After refmac, R = 0.2364 (Rfree = 0.000) for 3493 atoms. Found 55 (67 requested) and removed 35 (45 requested) atoms. Cycle 18: After refmac, R = 0.2323 (Rfree = 0.000) for 3510 atoms. Found 55 (66 requested) and removed 26 (45 requested) atoms. Cycle 19: After refmac, R = 0.2309 (Rfree = 0.000) for 3537 atoms. Found 48 (66 requested) and removed 38 (46 requested) atoms. Cycle 20: After refmac, R = 0.2288 (Rfree = 0.000) for 3546 atoms. Found 43 (64 requested) and removed 35 (46 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.90 1.68 Round 1: 390 peptides, 6 chains. Longest chain 109 peptides. Score 0.916 Round 2: 393 peptides, 6 chains. Longest chain 114 peptides. Score 0.918 Round 3: 395 peptides, 6 chains. Longest chain 179 peptides. Score 0.919 Round 4: 393 peptides, 6 chains. Longest chain 186 peptides. Score 0.918 Round 5: 390 peptides, 9 chains. Longest chain 72 peptides. Score 0.904 Taking the results from Round 3 Chains 6, Residues 389, Estimated correctness of the model 99.0 % 5 chains (385 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 198 A and 201 A Built loop between residues 130 B and 133 B Built loop between residues 179 B and 182 B 3 chains (395 residues) following loop building 2 chains (391 residues) in sequence following loop building ------------------------------------------------------ 29472 reflections ( 99.51 % complete ) and 3357 restraints for refining 3460 atoms. 409 conditional restraints added. Observations/parameters ratio is 2.13 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2448 (Rfree = 0.000) for 3460 atoms. Found 61 (61 requested) and removed 49 (45 requested) atoms. Cycle 22: After refmac, R = 0.2389 (Rfree = 0.000) for 3470 atoms. Found 57 (59 requested) and removed 25 (45 requested) atoms. Cycle 23: After refmac, R = 0.2335 (Rfree = 0.000) for 3500 atoms. Found 45 (60 requested) and removed 25 (45 requested) atoms. Cycle 24: After refmac, R = 0.2300 (Rfree = 0.000) for 3519 atoms. Found 46 (58 requested) and removed 23 (45 requested) atoms. Cycle 25: After refmac, R = 0.2286 (Rfree = 0.000) for 3541 atoms. Found 39 (59 requested) and removed 28 (46 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.91 1.69 Round 1: 386 peptides, 8 chains. Longest chain 75 peptides. Score 0.906 Round 2: 390 peptides, 8 chains. Longest chain 104 peptides. Score 0.908 Round 3: 390 peptides, 5 chains. Longest chain 180 peptides. Score 0.920 Round 4: 390 peptides, 7 chains. Longest chain 79 peptides. Score 0.912 Round 5: 392 peptides, 9 chains. Longest chain 95 peptides. Score 0.905 Taking the results from Round 3 Chains 5, Residues 385, Estimated correctness of the model 99.1 % 4 chains (378 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 87 A and 94 A Built loop between residues 180 B and 183 B 3 chains (393 residues) following loop building 2 chains (386 residues) in sequence following loop building ------------------------------------------------------ 29472 reflections ( 99.51 % complete ) and 3394 restraints for refining 3467 atoms. 460 conditional restraints added. Observations/parameters ratio is 2.13 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2442 (Rfree = 0.000) for 3467 atoms. Found 56 (56 requested) and removed 49 (45 requested) atoms. Cycle 27: After refmac, R = 0.2380 (Rfree = 0.000) for 3473 atoms. Found 54 (54 requested) and removed 21 (45 requested) atoms. Cycle 28: After refmac, R = 0.2328 (Rfree = 0.000) for 3506 atoms. Found 50 (55 requested) and removed 29 (45 requested) atoms. Cycle 29: After refmac, R = 0.2305 (Rfree = 0.000) for 3527 atoms. Found 53 (53 requested) and removed 31 (46 requested) atoms. Cycle 30: After refmac, R = 0.2299 (Rfree = 0.000) for 3548 atoms. Found 41 (52 requested) and removed 41 (46 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.90 1.68 Round 1: 391 peptides, 6 chains. Longest chain 180 peptides. Score 0.917 Round 2: 394 peptides, 7 chains. Longest chain 116 peptides. Score 0.914 Round 3: 394 peptides, 7 chains. Longest chain 116 peptides. Score 0.914 Round 4: 386 peptides, 9 chains. Longest chain 129 peptides. Score 0.902 Round 5: 392 peptides, 8 chains. Longest chain 122 peptides. Score 0.909 Taking the results from Round 1 Chains 6, Residues 385, Estimated correctness of the model 99.0 % 5 chains (381 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 61 A and 64 A Built loop between residues 97 A and 102 A Built loop between residues 180 B and 183 B 3 chains (393 residues) following loop building 2 chains (389 residues) in sequence following loop building ------------------------------------------------------ 29472 reflections ( 99.51 % complete ) and 3417 restraints for refining 3473 atoms. 480 conditional restraints added. Observations/parameters ratio is 2.12 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2391 (Rfree = 0.000) for 3473 atoms. Found 49 (49 requested) and removed 50 (45 requested) atoms. Cycle 32: After refmac, R = 0.2351 (Rfree = 0.000) for 3472 atoms. Found 47 (47 requested) and removed 17 (45 requested) atoms. Cycle 33: After refmac, R = 0.2304 (Rfree = 0.000) for 3501 atoms. Found 47 (47 requested) and removed 30 (45 requested) atoms. Cycle 34: After refmac, R = 0.2287 (Rfree = 0.000) for 3517 atoms. Found 41 (45 requested) and removed 35 (45 requested) atoms. Cycle 35: After refmac, R = 0.2272 (Rfree = 0.000) for 3522 atoms. Found 45 (45 requested) and removed 23 (45 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.89 1.67 Round 1: 390 peptides, 6 chains. Longest chain 180 peptides. Score 0.916 Round 2: 392 peptides, 5 chains. Longest chain 185 peptides. Score 0.921 Round 3: 392 peptides, 9 chains. Longest chain 72 peptides. Score 0.905 Round 4: 393 peptides, 7 chains. Longest chain 151 peptides. Score 0.914 Round 5: 390 peptides, 7 chains. Longest chain 121 peptides. Score 0.912 Taking the results from Round 2 Chains 5, Residues 387, Estimated correctness of the model 99.1 % 5 chains (387 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 26 B and 29 B Built loop between residues 128 B and 131 B Built loop between residues 179 B and 182 B 2 chains (393 residues) following loop building 2 chains (393 residues) in sequence following loop building ------------------------------------------------------ 29472 reflections ( 99.51 % complete ) and 3365 restraints for refining 3471 atoms. 409 conditional restraints added. Observations/parameters ratio is 2.12 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2400 (Rfree = 0.000) for 3471 atoms. Found 45 (45 requested) and removed 49 (45 requested) atoms. Cycle 37: After refmac, R = 0.2331 (Rfree = 0.000) for 3467 atoms. Found 45 (45 requested) and removed 17 (45 requested) atoms. Cycle 38: After refmac, R = 0.2301 (Rfree = 0.000) for 3495 atoms. Found 45 (45 requested) and removed 22 (45 requested) atoms. Cycle 39: After refmac, R = 0.2283 (Rfree = 0.000) for 3517 atoms. Found 45 (45 requested) and removed 32 (45 requested) atoms. Cycle 40: After refmac, R = 0.2266 (Rfree = 0.000) for 3529 atoms. Found 40 (46 requested) and removed 30 (46 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.89 1.67 Round 1: 391 peptides, 7 chains. Longest chain 75 peptides. Score 0.913 Round 2: 393 peptides, 6 chains. Longest chain 114 peptides. Score 0.918 Round 3: 393 peptides, 6 chains. Longest chain 153 peptides. Score 0.918 Round 4: 389 peptides, 7 chains. Longest chain 146 peptides. Score 0.911 Round 5: 390 peptides, 10 chains. Longest chain 63 peptides. Score 0.900 Taking the results from Round 3 Chains 7, Residues 387, Estimated correctness of the model 99.0 % 5 chains (380 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 86 A and 89 A Built loop between residues 26 B and 29 B Built loop between residues 177 B and 183 B 3 chains (393 residues) following loop building 2 chains (389 residues) in sequence following loop building ------------------------------------------------------ 29472 reflections ( 99.51 % complete ) and 3383 restraints for refining 3473 atoms. 451 conditional restraints added. Observations/parameters ratio is 2.12 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2433 (Rfree = 0.000) for 3473 atoms. Found 45 (45 requested) and removed 50 (45 requested) atoms. Cycle 42: After refmac, R = 0.2354 (Rfree = 0.000) for 3466 atoms. Found 45 (45 requested) and removed 16 (45 requested) atoms. Cycle 43: After refmac, R = 0.2303 (Rfree = 0.000) for 3494 atoms. Found 45 (45 requested) and removed 22 (45 requested) atoms. Cycle 44: After refmac, R = 0.2279 (Rfree = 0.000) for 3517 atoms. Found 37 (45 requested) and removed 27 (45 requested) atoms. Cycle 45: After refmac, R = 0.2255 (Rfree = 0.000) for 3526 atoms. Found 42 (46 requested) and removed 27 (46 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.89 1.67 Round 1: 388 peptides, 7 chains. Longest chain 89 peptides. Score 0.911 Round 2: 391 peptides, 8 chains. Longest chain 114 peptides. Score 0.909 Round 3: 394 peptides, 6 chains. Longest chain 136 peptides. Score 0.918 Round 4: 391 peptides, 9 chains. Longest chain 79 peptides. Score 0.905 Round 5: 387 peptides, 10 chains. Longest chain 75 peptides. Score 0.898 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 7, Residues 388, Estimated correctness of the model 99.0 % 5 chains (383 residues) have been docked in sequence Sequence coverage is 98 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 156 A and 159 A Built loop between residues 57 B and 60 B Built loop between residues 180 B and 185 B 3 chains (394 residues) following loop building 2 chains (391 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 29472 reflections ( 99.51 % complete ) and 2945 restraints for refining 2905 atoms. Observations/parameters ratio is 2.54 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3087 (Rfree = 0.000) for 2905 atoms. Found 37 (37 requested) and removed 0 (37 requested) atoms. Cycle 47: After refmac, R = 0.2881 (Rfree = 0.000) for 2905 atoms. Found 19 (38 requested) and removed 1 (38 requested) atoms. Cycle 48: After refmac, R = 0.2794 (Rfree = 0.000) for 2905 atoms. Found 8 (38 requested) and removed 4 (38 requested) atoms. Cycle 49: After refmac, R = 0.2759 (Rfree = 0.000) for 2905 atoms. Found 8 (38 requested) and removed 6 (38 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:29:42 GMT 2018 Job finished. TimeTaking 66.67 Used memory is bytes: 22932888