Sun 23 Dec 22:22:46 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 1zy9-2.3-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1zy9-2.3-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1zy9-2.3-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1zy9-2.3-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/1zy9-2.3-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1zy9-2.3-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 22:22:56 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/1zy9-2.3-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1zy9-2.3-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 768 and 0 Target number of residues in the AU: 768 Target solvent content: 0.5189 Checking the provided sequence file Detected sequence length: 564 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 564 Adjusted target solvent content: 0.65 Input MTZ file: 1zy9-2.3-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: 20 Cell parameters: 121.755 160.844 88.238 90.000 90.000 90.000 Input sequence file: 1zy9-2.3-parrot-hancs.fasta_lf Building free atoms model in initial map for 4512 target number of atoms Had to go as low as 0.55 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 Loops will be built when appropriate and at the last cycle Resolution range: 97.078 2.340 Wilson plot Bfac: 27.59 36098 reflections ( 97.78 % complete ) and 0 restraints for refining 5048 atoms. Observations/parameters ratio is 1.79 ------------------------------------------------------ Starting model: R = 0.3269 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2645 (Rfree = 0.000) for 5048 atoms. Found 110 (110 requested) and removed 71 (55 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.30 1.87 Round 1: 381 peptides, 58 chains. Longest chain 15 peptides. Score 0.468 Round 2: 433 peptides, 42 chains. Longest chain 34 peptides. Score 0.654 Round 3: 460 peptides, 31 chains. Longest chain 48 peptides. Score 0.744 Round 4: 480 peptides, 31 chains. Longest chain 41 peptides. Score 0.763 Round 5: 480 peptides, 21 chains. Longest chain 69 peptides. Score 0.808 Taking the results from Round 5 Chains 31, Residues 459, Estimated correctness of the model 94.3 % 11 chains (334 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 233 A and 241 A Built loop between residues 279 A and 285 A Built loop between residues 366 A and 369 A Built loop between residues 479 A and 483 A Built loop between residues 501 A and 508 A 21 chains (474 residues) following loop building 6 chains (357 residues) in sequence following loop building ------------------------------------------------------ 36098 reflections ( 97.78 % complete ) and 6030 restraints for refining 4692 atoms. 2624 conditional restraints added. Observations/parameters ratio is 1.92 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2865 (Rfree = 0.000) for 4692 atoms. Found 102 (102 requested) and removed 72 (51 requested) atoms. Cycle 2: After refmac, R = 0.2572 (Rfree = 0.000) for 4652 atoms. Found 101 (101 requested) and removed 59 (51 requested) atoms. Cycle 3: After refmac, R = 0.2389 (Rfree = 0.000) for 4652 atoms. Found 98 (98 requested) and removed 54 (51 requested) atoms. Cycle 4: After refmac, R = 0.2258 (Rfree = 0.000) for 4664 atoms. Found 96 (96 requested) and removed 51 (51 requested) atoms. Cycle 5: After refmac, R = 0.2130 (Rfree = 0.000) for 4680 atoms. Found 95 (95 requested) and removed 52 (51 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.27 1.85 Round 1: 500 peptides, 14 chains. Longest chain 127 peptides. Score 0.849 Round 2: 513 peptides, 13 chains. Longest chain 96 peptides. Score 0.861 Round 3: 518 peptides, 10 chains. Longest chain 205 peptides. Score 0.874 Round 4: 512 peptides, 9 chains. Longest chain 106 peptides. Score 0.874 Round 5: 511 peptides, 13 chains. Longest chain 87 peptides. Score 0.860 Taking the results from Round 4 Chains 10, Residues 503, Estimated correctness of the model 97.4 % 7 chains (485 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 195 A and 199 A Built loop between residues 237 A and 240 A Built loop between residues 288 A and 291 A Built loop between residues 334 A and 337 A Built loop between residues 441 A and 444 A 5 chains (514 residues) following loop building 2 chains (496 residues) in sequence following loop building ------------------------------------------------------ 36098 reflections ( 97.78 % complete ) and 4649 restraints for refining 4664 atoms. 445 conditional restraints added. Observations/parameters ratio is 1.93 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1989 (Rfree = 0.000) for 4664 atoms. Found 92 (92 requested) and removed 53 (51 requested) atoms. Cycle 7: After refmac, R = 0.1802 (Rfree = 0.000) for 4674 atoms. Found 90 (90 requested) and removed 53 (51 requested) atoms. Cycle 8: After refmac, R = 0.1712 (Rfree = 0.000) for 4693 atoms. Found 89 (89 requested) and removed 53 (51 requested) atoms. Cycle 9: After refmac, R = 0.1651 (Rfree = 0.000) for 4718 atoms. Found 87 (87 requested) and removed 54 (51 requested) atoms. Cycle 10: After refmac, R = 0.1605 (Rfree = 0.000) for 4736 atoms. Found 85 (85 requested) and removed 53 (52 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.26 1.84 Round 1: 521 peptides, 4 chains. Longest chain 277 peptides. Score 0.895 Round 2: 523 peptides, 2 chains. Longest chain 325 peptides. Score 0.902 Round 3: 514 peptides, 7 chains. Longest chain 239 peptides. Score 0.882 Round 4: 519 peptides, 4 chains. Longest chain 397 peptides. Score 0.894 Round 5: 513 peptides, 11 chains. Longest chain 111 peptides. Score 0.868 Taking the results from Round 2 Chains 2, Residues 521, Estimated correctness of the model 98.3 % 2 chains (521 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 209 A and 212 A 1 chains (523 residues) following loop building 1 chains (523 residues) in sequence following loop building ------------------------------------------------------ 36098 reflections ( 97.78 % complete ) and 4495 restraints for refining 4649 atoms. 128 conditional restraints added. Observations/parameters ratio is 1.94 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1717 (Rfree = 0.000) for 4649 atoms. Found 81 (81 requested) and removed 51 (50 requested) atoms. Cycle 12: After refmac, R = 0.1593 (Rfree = 0.000) for 4673 atoms. Found 80 (80 requested) and removed 55 (51 requested) atoms. Cycle 13: After refmac, R = 0.1547 (Rfree = 0.000) for 4692 atoms. Found 78 (78 requested) and removed 52 (51 requested) atoms. Cycle 14: After refmac, R = 0.1524 (Rfree = 0.000) for 4714 atoms. Found 76 (76 requested) and removed 59 (51 requested) atoms. Cycle 15: After refmac, R = 0.1508 (Rfree = 0.000) for 4729 atoms. Found 74 (74 requested) and removed 58 (51 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.27 1.85 Round 1: 521 peptides, 3 chains. Longest chain 310 peptides. Score 0.898 Round 2: 521 peptides, 4 chains. Longest chain 264 peptides. Score 0.895 Round 3: 516 peptides, 5 chains. Longest chain 264 peptides. Score 0.889 Round 4: 517 peptides, 9 chains. Longest chain 133 peptides. Score 0.877 Round 5: 512 peptides, 10 chains. Longest chain 139 peptides. Score 0.871 Taking the results from Round 1 Chains 3, Residues 518, Estimated correctness of the model 98.2 % 3 chains (518 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 321 A and 324 A Built loop between residues 474 A and 478 A 1 chains (523 residues) following loop building 1 chains (523 residues) in sequence following loop building ------------------------------------------------------ 36098 reflections ( 97.78 % complete ) and 4491 restraints for refining 4620 atoms. 124 conditional restraints added. Observations/parameters ratio is 1.95 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1650 (Rfree = 0.000) for 4620 atoms. Found 71 (71 requested) and removed 51 (50 requested) atoms. Cycle 17: After refmac, R = 0.1542 (Rfree = 0.000) for 4635 atoms. Found 69 (69 requested) and removed 50 (50 requested) atoms. Cycle 18: After refmac, R = 0.1514 (Rfree = 0.000) for 4650 atoms. Found 67 (67 requested) and removed 52 (50 requested) atoms. Cycle 19: After refmac, R = 0.1489 (Rfree = 0.000) for 4663 atoms. Found 65 (65 requested) and removed 55 (51 requested) atoms. Cycle 20: After refmac, R = 0.1473 (Rfree = 0.000) for 4672 atoms. Found 63 (63 requested) and removed 53 (51 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.27 1.85 Round 1: 523 peptides, 1 chains. Longest chain 523 peptides. Score 0.905 Round 2: 522 peptides, 3 chains. Longest chain 278 peptides. Score 0.898 Round 3: 516 peptides, 5 chains. Longest chain 264 peptides. Score 0.889 Round 4: 518 peptides, 6 chains. Longest chain 223 peptides. Score 0.887 Round 5: 520 peptides, 6 chains. Longest chain 224 peptides. Score 0.888 Taking the results from Round 1 Chains 4, Residues 522, Estimated correctness of the model 98.4 % 2 chains (514 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 496 A and 503 A 2 chains (523 residues) following loop building 1 chains (520 residues) in sequence following loop building ------------------------------------------------------ 36098 reflections ( 97.78 % complete ) and 4579 restraints for refining 4655 atoms. 229 conditional restraints added. Observations/parameters ratio is 1.94 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1734 (Rfree = 0.000) for 4655 atoms. Found 61 (61 requested) and removed 61 (50 requested) atoms. Cycle 22: After refmac, R = 0.1595 (Rfree = 0.000) for 4650 atoms. Found 59 (59 requested) and removed 53 (50 requested) atoms. Cycle 23: After refmac, R = 0.1557 (Rfree = 0.000) for 4655 atoms. Found 57 (57 requested) and removed 54 (50 requested) atoms. Cycle 24: After refmac, R = 0.1528 (Rfree = 0.000) for 4658 atoms. Found 55 (55 requested) and removed 53 (50 requested) atoms. Cycle 25: After refmac, R = 0.1509 (Rfree = 0.000) for 4659 atoms. Found 53 (53 requested) and removed 55 (51 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.26 1.84 Round 1: 523 peptides, 2 chains. Longest chain 492 peptides. Score 0.902 Round 2: 522 peptides, 3 chains. Longest chain 277 peptides. Score 0.898 Round 3: 518 peptides, 7 chains. Longest chain 264 peptides. Score 0.884 Round 4: 515 peptides, 11 chains. Longest chain 78 peptides. Score 0.869 Round 5: 519 peptides, 5 chains. Longest chain 264 peptides. Score 0.891 Taking the results from Round 1 Chains 2, Residues 521, Estimated correctness of the model 98.3 % 2 chains (521 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 42 A and 45 A 1 chains (523 residues) following loop building 1 chains (523 residues) in sequence following loop building ------------------------------------------------------ 36098 reflections ( 97.78 % complete ) and 4510 restraints for refining 4620 atoms. 143 conditional restraints added. Observations/parameters ratio is 1.95 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1620 (Rfree = 0.000) for 4620 atoms. Found 50 (50 requested) and removed 51 (50 requested) atoms. Cycle 27: After refmac, R = 0.1533 (Rfree = 0.000) for 4616 atoms. Found 50 (50 requested) and removed 52 (50 requested) atoms. Cycle 28: After refmac, R = 0.1505 (Rfree = 0.000) for 4612 atoms. Found 50 (50 requested) and removed 44 (50 requested) atoms. Cycle 29: After refmac, R = 0.1483 (Rfree = 0.000) for 4618 atoms. Found 50 (50 requested) and removed 43 (50 requested) atoms. Cycle 30: After refmac, R = 0.1470 (Rfree = 0.000) for 4625 atoms. Found 50 (50 requested) and removed 49 (50 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.26 1.84 Round 1: 522 peptides, 3 chains. Longest chain 311 peptides. Score 0.898 Round 2: 522 peptides, 3 chains. Longest chain 264 peptides. Score 0.898 Round 3: 518 peptides, 4 chains. Longest chain 410 peptides. Score 0.893 Round 4: 517 peptides, 7 chains. Longest chain 221 peptides. Score 0.883 Round 5: 518 peptides, 7 chains. Longest chain 116 peptides. Score 0.884 Taking the results from Round 2 Chains 3, Residues 519, Estimated correctness of the model 98.2 % 3 chains (519 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 197 A and 200 A Built loop between residues 270 A and 273 A 1 chains (523 residues) following loop building 1 chains (523 residues) in sequence following loop building ------------------------------------------------------ 36098 reflections ( 97.78 % complete ) and 4480 restraints for refining 4608 atoms. 113 conditional restraints added. Observations/parameters ratio is 1.96 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1620 (Rfree = 0.000) for 4608 atoms. Found 50 (50 requested) and removed 52 (50 requested) atoms. Cycle 32: After refmac, R = 0.1536 (Rfree = 0.000) for 4605 atoms. Found 50 (50 requested) and removed 45 (50 requested) atoms. Cycle 33: After refmac, R = 0.1502 (Rfree = 0.000) for 4609 atoms. Found 50 (50 requested) and removed 47 (50 requested) atoms. Cycle 34: After refmac, R = 0.1494 (Rfree = 0.000) for 4611 atoms. Found 50 (50 requested) and removed 44 (50 requested) atoms. Cycle 35: After refmac, R = 0.1488 (Rfree = 0.000) for 4617 atoms. Found 50 (50 requested) and removed 50 (50 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.27 1.85 Round 1: 522 peptides, 2 chains. Longest chain 463 peptides. Score 0.901 Round 2: 521 peptides, 4 chains. Longest chain 338 peptides. Score 0.895 Round 3: 517 peptides, 7 chains. Longest chain 128 peptides. Score 0.883 Round 4: 519 peptides, 6 chains. Longest chain 236 peptides. Score 0.888 Round 5: 518 peptides, 7 chains. Longest chain 167 peptides. Score 0.884 Taking the results from Round 1 Chains 2, Residues 520, Estimated correctness of the model 98.3 % 2 chains (520 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 474 A and 478 A 1 chains (523 residues) following loop building 1 chains (523 residues) in sequence following loop building ------------------------------------------------------ 36098 reflections ( 97.78 % complete ) and 4477 restraints for refining 4604 atoms. 110 conditional restraints added. Observations/parameters ratio is 1.96 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1621 (Rfree = 0.000) for 4604 atoms. Found 50 (50 requested) and removed 50 (50 requested) atoms. Cycle 37: After refmac, R = 0.1527 (Rfree = 0.000) for 4603 atoms. Found 50 (50 requested) and removed 44 (50 requested) atoms. Cycle 38: After refmac, R = 0.1494 (Rfree = 0.000) for 4608 atoms. Found 50 (50 requested) and removed 45 (50 requested) atoms. Cycle 39: After refmac, R = 0.1486 (Rfree = 0.000) for 4611 atoms. Found 50 (50 requested) and removed 44 (50 requested) atoms. Cycle 40: After refmac, R = 0.1471 (Rfree = 0.000) for 4617 atoms. Found 50 (50 requested) and removed 52 (50 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.25 1.83 Round 1: 524 peptides, 2 chains. Longest chain 311 peptides. Score 0.902 Round 2: 523 peptides, 2 chains. Longest chain 338 peptides. Score 0.902 Round 3: 517 peptides, 5 chains. Longest chain 223 peptides. Score 0.890 Round 4: 517 peptides, 8 chains. Longest chain 190 peptides. Score 0.880 Round 5: 521 peptides, 6 chains. Longest chain 193 peptides. Score 0.889 Taking the results from Round 2 Chains 2, Residues 521, Estimated correctness of the model 98.3 % 2 chains (521 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 196 A and 199 A 1 chains (523 residues) following loop building 1 chains (523 residues) in sequence following loop building ------------------------------------------------------ 36098 reflections ( 97.78 % complete ) and 4497 restraints for refining 4613 atoms. 130 conditional restraints added. Observations/parameters ratio is 1.96 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1609 (Rfree = 0.000) for 4613 atoms. Found 50 (50 requested) and removed 53 (50 requested) atoms. Cycle 42: After refmac, R = 0.1531 (Rfree = 0.000) for 4608 atoms. Found 50 (50 requested) and removed 42 (50 requested) atoms. Cycle 43: After refmac, R = 0.1491 (Rfree = 0.000) for 4614 atoms. Found 50 (50 requested) and removed 49 (50 requested) atoms. Cycle 44: After refmac, R = 0.1471 (Rfree = 0.000) for 4614 atoms. Found 50 (50 requested) and removed 51 (50 requested) atoms. Cycle 45: After refmac, R = 0.1466 (Rfree = 0.000) for 4611 atoms. Found 50 (50 requested) and removed 52 (50 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.26 1.84 Round 1: 524 peptides, 2 chains. Longest chain 310 peptides. Score 0.902 Round 2: 522 peptides, 4 chains. Longest chain 231 peptides. Score 0.895 Round 3: 512 peptides, 5 chains. Longest chain 325 peptides. Score 0.887 Round 4: 520 peptides, 5 chains. Longest chain 264 peptides. Score 0.891 Round 5: 512 peptides, 12 chains. Longest chain 96 peptides. Score 0.864 Taking the results from Round 1 Last building cycle: Chain fragments will be rearranged Chains 2, Residues 522, Estimated correctness of the model 98.3 % 2 chains (522 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 321 A and 324 A 1 chains (524 residues) following loop building 1 chains (524 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 36098 reflections ( 97.78 % complete ) and 4376 restraints for refining 4259 atoms. Observations/parameters ratio is 2.12 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1934 (Rfree = 0.000) for 4259 atoms. Found 46 (46 requested) and removed 0 (46 requested) atoms. Cycle 47: After refmac, R = 0.1782 (Rfree = 0.000) for 4259 atoms. Found 47 (47 requested) and removed 0 (47 requested) atoms. Cycle 48: After refmac, R = 0.1694 (Rfree = 0.000) for 4259 atoms. Found 44 (47 requested) and removed 2 (47 requested) atoms. Cycle 49: After refmac, R = 0.1640 (Rfree = 0.000) for 4259 atoms. TimeTaking 87.97